Wed, 15 Aug 2018

Package SPUTNIK updated to version 1.0.3.2 with previous version 1.0.3.1 dated 2018-07-20

Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>

Diff between SPUTNIK versions 1.0.3.1 dated 2018-07-20 and 1.0.3.2 dated 2018-08-15

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Package filesstrings updated to version 2.6.0 with previous version 2.5.0 dated 2018-06-29

Title: Handy File and String Manipulation
Description: Convenient functions for moving files, deleting directories, and a variety of string operations that facilitate manipulating files and extracting information from strings.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>), Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between filesstrings versions 2.5.0 dated 2018-06-29 and 2.6.0 dated 2018-08-15

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Package distances updated to version 0.1.4 with previous version 0.1.3 dated 2018-07-20

Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between distances versions 0.1.3 dated 2018-07-20 and 0.1.4 dated 2018-08-15

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Package rpdo updated to version 0.2.4 with previous version 0.2.3 dated 2018-01-31

Title: Pacific Decadal Oscillation Index Data
Description: Monthly Pacific Decadal Oscillation (PDO) index values from January 1900 to present.
Author: Joe Thorley [aut, cre], Nathan Mantua [aut, dtc], Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between rpdo versions 0.2.3 dated 2018-01-31 and 0.2.4 dated 2018-08-15

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Package echo.find updated to version 1.3.1 with previous version 1.2.1 dated 2018-07-24

Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators (ECHO)
Description: Provides a function (echo_find()) designed to find rhythms from data using extended harmonic oscillators. For more information, see H. De los Santos et al. (2017) <doi:10.1145/3107411.3107420> .
Author: Hannah De los Santos [aut, cre], Emily Collins [aut], Jonathan Shewchuk [ctb], E.F. Harding [ctb], Kristin Bennett [aut], Jennifer Hurley [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>

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Package tensr updated to version 1.0.1 with previous version 1.0.0 dated 2016-02-03

Title: Covariance Inference and Decompositions for Tensor Datasets
Description: A collection of functions for Kronecker structured covariance estimation and testing under the array normal model. For estimation, maximum likelihood and Bayesian equivariant estimation procedures are implemented. For testing, a likelihood ratio testing procedure is available. This package also contains additional functions for manipulating and decomposing tensor data sets. This work was partially supported by NSF grant DMS-1505136. Details of the methods are described in Gerard and Hoff (2015) <doi:10.1016/j.jmva.2015.01.020> and Gerard and Hoff (2016) <doi:10.1016/j.laa.2016.04.033>.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>), Peter Hoff [aut]
Maintainer: David Gerard <gerard.1787@gmail.com>

Diff between tensr versions 1.0.0 dated 2016-02-03 and 1.0.1 dated 2018-08-15

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Package NormalBetaPrime updated to version 1.1 with previous version 1.0 dated 2018-07-22

Title: Normal Beta Prime Prior
Description: Implements Bayesian linear regression, variable selection, normal means estimation, and multiple hypothesis testing using the normal-beta prime prior, as introduced by Bai and Ghosh (2018) <arXiv:1807.02421> and Bai and Ghosh (2018) <arXiv:1807.06539>. Normal means estimation and multiple testing for the Dirichlet-Laplace <doi:10.1080/01621459.2014.960967> and horseshoe+ priors <doi:10.1214/16-BA1028> are also available in this package.
Author: Ray Bai, Malay Ghosh
Maintainer: Ray Bai <raybai07@ufl.edu>

Diff between NormalBetaPrime versions 1.0 dated 2018-07-22 and 1.1 dated 2018-08-15

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Package HEMDAG updated to version 2.2.3 with previous version 2.1.3 dated 2018-05-21

Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of Hierarchical Ensemble Methods for Directed Acyclic Graphs (DAGs). The 'HEMDAG' package can be used to enhance the predictions of virtually any flat learning methods, by taking into account the hierarchical nature of the classes of a bio-ontology. 'HEMDAG' is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>), Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>), Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>

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Package choroplethr updated to version 3.6.3 with previous version 3.6.2 dated 2018-06-21

Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps.
Author: Ari Lamstein [aut, cre], Brian Johnson [ctb], Trulia, Inc. [cph]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>

Diff between choroplethr versions 3.6.2 dated 2018-06-21 and 3.6.3 dated 2018-08-15

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Package cholera updated to version 0.5.1 with previous version 0.5.0 dated 2018-07-16

Title: Amend, Augment and Aid Analysis of John Snow's Cholera Map
Description: Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>

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Package BMisc updated to version 1.3.1 with previous version 1.3.0 dated 2018-07-16

Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing Results
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas.
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>

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Package vetr updated to version 0.2.6 with previous version 0.2.5 dated 2018-06-23

Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects meet structural requirements, and auto-composing error messages when they do not.
Author: Brodie Gaslam [aut, cre], Paxdiablo [cph] (Hash table implementation in src/pfhash.h), R Core Team [cph] (Used/adapted several code snippets from R sources, see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>

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Package sybil updated to version 2.1.2 with previous version 2.1.1 dated 2018-05-14

Title: Efficient Constrained Based Modelling
Description: This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
Author: Mayo Roettger [cre], Gabriel Gelius-Dietrich [aut], C. Jonathan Fritzemeier [ctb], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb], Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb], Martin J. Lercher [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>

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Package spdep updated to version 0.7-8 with previous version 0.7-7 dated 2018-04-03

Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I', 'APLE', 'Gearys C', 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' Index, 'Getis/Ord' G and multicoloured join count statistics, local 'Moran's I' and 'Getis/Ord' G, 'saddlepoint' approximations, exact tests for global and local 'Moran's I' and 'LOSH' local indicators of spatial heteroscedasticity; and functions for estimating spatial simultaneous 'autoregressive' ('SAR') lag and error models, impact measures for lag models, weighted and 'unweighted' 'SAR' and 'CAR' spatial regression models, semi-parametric and Moran 'eigenvector' spatial filtering, 'GM SAR' error models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Micah Altman [ctb], Luc Anselin [ctb], Renato Assunção [ctb], Olaf Berke [ctb], Andrew Bernat [ctb], Guillaume Blanchet [ctb], Eric Blankmeyer [ctb], Marilia Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb], Carsten Dormann [ctb], Stéphane Dray [ctb], Virgilio Gómez-Rubio [ctb], Martin Gubri [ctb], Rein Halbersma [ctb], Elias Krainski [ctb], Pierre Legendre [ctb], Nicholas Lewin-Koh [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Abhirup Mallik [ctb, trl], Giovanni Millo [ctb], Werner Mueller [ctb], Hisaji Ono [ctb], Pedro Peres-Neto [ctb], Gianfranco Piras [ctb], Markus Reder [ctb], Michael Tiefelsdorf [ctb], René Westerholt [ctb], Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package stilt updated to version 1.3.0 with previous version 1.2.0 dated 2017-11-02

Title: Separable Gaussian Process Interpolation (Emulation)
Description: Functions for simplified emulation of time series computer model output in model parameter space using Gaussian processes. Stilt can be used more generally for Kriging of spatio-temporal fields. There are functions to predict at new parameter settings, to test the emulator using cross-validation (which includes information on 95% confidence interval empirical coverage), and to produce contour plots over 2D slices in model parameter space.
Author: Roman Olson, Won Chang, Klaus Keller, and Murali Haran
Maintainer: Kelsey Ruckert <datamgmt@scrim.psu.edu>

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Package BayesGOF updated to version 4.2 with previous version 4.0 dated 2018-05-17

Title: Bayesian Modeling via Goodness-of-Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>

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Package texPreview updated to version 1.1.5 with previous version 1.1.4 dated 2018-06-07

Title: Compile and Preview Snippets of 'LaTeX' in 'RStudio'
Description: Compile and preview snippets of 'LaTeX'. Can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents. Must have 'pdflatex' or 'xelatex' or 'lualatex' in 'PATH'.
Author: Jonathan Sidi [aut, cre], Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>

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Package RSuite updated to version 0.32-244 with previous version 0.31-243 dated 2018-07-26

Title: Supports Developing, Building and Deploying R Solution
Description: Supports safe and reproducible solutions development in R. It will help you with environment separation per project, dependency management, local packages creation and preparing deployment packs for your solutions.
Author: Walerian Sokolowski [aut, cre], Wit Jakuczun [aut], Yulia Yakimechko [aut], Mateusz Kalinowski [aut], Ryszard Szymanski [aut], WLOG Solutions [cph], R Consortium [ctb] (Definitions of system requirements are taken from sysreqsdb project.)
Maintainer: Walerian Sokolowski <rsuite@wlogsolutions.com>

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Package psidR updated to version 1.6 with previous version 1.5 dated 2018-04-20

Title: Build Panel Data Sets from PSID Raw Data
Description: Makes it easy to build panel data in wide format from Panel Survey of Income Dynamics ('PSID') delivered raw data. Deals with data downloaded and pre-processed by 'Stata' or 'SAS', or can optionally download directly from the PSID server using the 'SAScii' package. 'psidR' takes care of merging data from each wave onto a cross-period index file, so that individuals can be followed over time. The user must specify which years they are interested in, and the 'PSID' variable names (e.g. ER21003) for each year (they differ in each year). The package offers helper functions to retrieve variable names from different waves. There are different panel data designs and sample subsetting criteria implemented ("SRC", "SEO", "immigrant" and "latino" samples).
Author: Florian Oswald
Maintainer: Florian Oswald <florian.oswald@gmail.com>

Diff between psidR versions 1.5 dated 2018-04-20 and 1.6 dated 2018-08-15

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Package PMCMRplus updated to version 1.4.0 with previous version 1.3.0 dated 2018-07-28

Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended
Description: For one-way layout experiments the one-way ANOVA can be performed as an omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test, Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally distributed residuals and equal within variance are available. Furthermore, all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for normally distributed residuals and heterogeneous variances are provided. Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one tests is provided for non-normally distributed residuals and homogeneous variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and all-pairs tests (Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test, Dunn test, U-test) are given for the analysis of variance by ranks. Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra test, Spearman test) are included. In addition, a Friedman-test for one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack test for unbalanced CRBD is provided with consequent all-pairs tests (Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and many-to-one tests (Nemenyi test, Demsar test, Exact test). A trend can be tested with Pages's test. Durbin's test for a two-way balanced incomplete block design (BIBD) is given in this package as well as Gore's test for CRBD with multiple observations per cell is given. Outlier tests, Mandel's k- and h statistic as well as functions for Type I error and Power analysis as well as generic summary, print and plot methods are provided.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

Diff between PMCMRplus versions 1.3.0 dated 2018-07-28 and 1.4.0 dated 2018-08-15

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More information about PMCMRplus at CRAN
Permanent link

Package mumm updated to version 0.2.1 with previous version 0.2.0 dated 2018-07-01

Title: Multiplicative Mixed Models using the Template Model Builder
Description: Fit multiplicative mixed models using maximum likelihood estimation via the Template Model Builder (TMB), Kristensen K, Nielsen A, Berg CW, Skaug H, Bell BM (2016) <doi:10.18637/jss.v070.i05>. One version of the multiplicative mixed model is applied in Piepho (1999) <doi:10.1111/j.0006-341X.1999.01120.x>. The package provides functions for calculating confidence intervals for the model parameters and for performing likelihood ratio tests.
Author: Sofie Poedenphant [aut, cre], Per Bruun Brockhoff [aut]
Maintainer: Sofie Poedenphant <sofp@dtu.dk>

Diff between mumm versions 0.2.0 dated 2018-07-01 and 0.2.1 dated 2018-08-15

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More information about mumm at CRAN
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Package helminthR updated to version 1.0.6 with previous version 1.0.5 dated 2018-07-30

Title: Access London Natural History Museum Host-Helminth Record Database
Description: Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides a programmatic interface to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently <http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>. The package allows the user to query by host species, parasite species, and geographic location.
Author: Tad Dallas
Maintainer: Tad Dallas <tad.a.dallas@gmail.com>

Diff between helminthR versions 1.0.5 dated 2018-07-30 and 1.0.6 dated 2018-08-15

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Package ENMeval updated to version 0.3.0 with previous version 0.2.2 dated 2017-01-10

Title: Automated Runs and Evaluations of Ecological Niche Models
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006) or maxnet (Phillips et al. 2017).
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella <bob.muscarella@gmail.com>

Diff between ENMeval versions 0.2.2 dated 2017-01-10 and 0.3.0 dated 2018-08-15

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Package phreeqc updated to version 3.4.9 with previous version 3.4.8 dated 2018-08-14

Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh, R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>

Diff between phreeqc versions 3.4.8 dated 2018-08-14 and 3.4.9 dated 2018-08-15

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More information about phreeqc at CRAN
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Package civis updated to version 1.5.1 with previous version 1.5.0 dated 2018-06-21

Title: R Client for the 'Civis data science API'
Description: A set of tools around common workflows and a convenient interface to make requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut], Keith Ingersoll [aut], Bill Lattner [ctb], Anh Le [ctb], Michelangelo D'Agostino [ctb], Sam Weiss [ctb], Stephen Hoover [ctb], Danning Chen [ctb], Elizabeth Sander [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>

Diff between civis versions 1.5.0 dated 2018-06-21 and 1.5.1 dated 2018-08-15

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Package bioacoustics updated to version 0.1.5 with previous version 0.1.4 dated 2018-08-09

Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, Inc. [ctb, cph] (Read WAC files, original C code), WavX Inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>

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Package bomrang updated to version 0.3.0 with previous version 0.2.2 dated 2018-07-19

Title: Australian Government Bureau of Meteorology (BOM) Data from R
Description: Provides functions to interface with Australian Government Bureau of Meteorology (BOM) data, fetching data and returning a tidy data frame of précis forecasts, historical and current weather data from stations, agriculture bulletin data, BOM 0900 or 1500 weather bulletins or a raster stack object of satellite imagery from GeoTIFF files. Data (c) Australian Government Bureau of Meteorology Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See <http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>), Dean Marchiori [aut], Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>), Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>), Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>), James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>), Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package rquery updated to version 0.6.2 with previous version 0.6.1 dated 2018-08-01

Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible modeling step, explicit query reasoning and checking.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Tue, 14 Aug 2018

Package ohtadstats updated to version 1.2.1 with previous version 1.1.1 dated 2018-05-27

Title: Tomoka Ohta D Statistics
Description: Calculate's Tomoka Ohta's partitioning of linkage disequilibrium, deemed D-statistics, for pairs of loci. Beissinger et al. (2016) <doi:10.1038/hdy.2015.81>.
Author: Paul F. Petrowski <pfpetrowski@mail.missouri.edu> & Timothy M. Beissinger <timbeissinger@gmail.com>
Maintainer: Paul F. Petrowski <pfpetrowski@mail.missouri.edu>

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Package rplos updated to version 0.8.4 with previous version 0.8.2 dated 2018-07-19

Title: Interface to the Search API for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based search API (<http://api.plos.org/>) provided by the Public Library of Science journals to search their articles. Functions are included for searching for articles, retrieving articles, making plots, doing 'faceted' searches, 'highlight' searches, and viewing results of 'highlighted' searches in a browser.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package KScorrect updated to version 1.2.4 with previous version 1.2.3 dated 2018-03-04

Title: Lilliefors-Corrected Kolmogorov-Smirnov Goodness-of-Fit Tests
Description: Implements the Lilliefors-corrected Kolmogorov-Smirnov test for use in goodness-of-fit tests, suitable when population parameters are unknown and must be estimated by sample statistics. P-values are estimated by simulation. Can be used with a variety of continuous distributions, including normal, lognormal, univariate mixtures of normals, uniform, loguniform, exponential, gamma, and Weibull distributions. Functions to generate random numbers and calculate density, distribution, and quantile functions are provided for use with the log uniform and mixture distributions.
Author: Phil Novack-Gottshall, Steve C. Wang
Maintainer: Phil Novack-Gottshall <pnovack-gottshall@ben.edu>

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Package JointAI updated to version 0.3.0 with previous version 0.2.0 dated 2018-07-05

Title: Joint Analysis and Imputation of Incomplete Data
Description: Provides joint analysis and imputation of linear regression models, generalized linear regression models or linear mixed models with incomplete (covariate) data in the Bayesian framework. The package performs some preprocessing of the data and creates a 'JAGS' model, which will then automatically be passed to 'JAGS' <http://mcmc-jags.sourceforge.net> with the help of the package 'rjags'. It also provides summary and plotting functions for the output.
Author: Nicole S. Erler [aut, cre] (<https://orcid.org/0000-0002-9370-6832>)
Maintainer: Nicole S. Erler <n.erler@erasmusmc.nl>

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Package MALDIquantForeign updated to version 0.11.5 with previous version 0.11.1 dated 2017-12-04

Title: Import/Export Routines for 'MALDIquant'
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from 'MALDIquant' objects.
Author: Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

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Package Quandl updated to version 2.9.1 with previous version 2.8.0 dated 2016-04-23

Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, downloading a zip with all data from a Quandl database, and the ability to search. This R package uses the Quandl API. For more information go to <https://www.quandl.com/docs/api>. For more help on the package itself go to <https://www.quandl.com/help/r>.
Author: Raymond McTaggart [aut, cre], Gergely Daroczi [aut], Clement Leung [aut], Quandl Inc. [cph]
Maintainer: Raymond McTaggart <ray@quandl.com>

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Package pmmlTransformations updated to version 1.3.2 with previous version 1.3.1 dated 2017-02-27

Title: Transforms Input Data from a PMML Perspective
Description: Allows for data to be transformed before using it to construct models. Builds structures to allow functions in the PMML package to output transformation details in addition to the model in the resulting PMML file. The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms.
Author: Tridivesh Jena, Wen Ching Lin, Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@softwareag.com>

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Package kerasformula updated to version 1.5.0 with previous version 1.0.0 dated 2018-05-06

Title: A High-Level R Interface for Neural Nets
Description: Adds a high-level interface for 'keras' neural nets. kms() fits neural net and accepts R formulas to aid data munging and hyperparameter selection. kms() can optionally accept a compiled keras_sequential_model() from 'keras'. kms() accepts a number of parameters (like loss and optimizer) and splits the data into (optionally sparse) test and training matrices. kms() facilitates setting advanced hyperparameters (e.g., regularization). kms() returns a single object with predictions, a confusion matrix, and function call details.
Author: Pete Mohanty [aut, cre]
Maintainer: Pete Mohanty <pete.mohanty@gmail.com>

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Package ggstatsplot updated to version 0.0.5 with previous version 0.0.4 dated 2018-07-05

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests (parametric, non-parametric, or robust) included in the plots themselves. It is targeted primarily at behavioral sciences community to provide a one-line code to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms) or categorical (pie charts) data.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package WeMix updated to version 2.0.0 with previous version 1.0.2 dated 2018-04-10

Title: Weighted Mixed-Effects Models, using Multilevel Pseudo Maximum Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a Weighted Mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. The model is fit using adaptive quadrature.
Author: Paul Bailey, Claire Kelley, Trang Nguyen, Huade Huo.
Maintainer: Claire Kelley <ckelley@air.org>

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Package ProliferativeIndex updated to version 1.0.1 with previous version 1.0.0 dated 2017-02-16

Title: Calculates and Analyzes the Proliferative Index
Description: Provides functions for calculating and analyzing the proliferative index (PI) from an RNA-seq dataset. As described in Ramaker & Lasseigne, et al. bioRxiv, 2016 <doi:10.1101/063057>.
Author: Brittany Lasseigne [aut, cre], Ryne Ramaker [aut]
Maintainer: Brittany Lasseigne <brittany.lasseigne@gmail.com>

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Package rcompanion updated to version 2.0.0 with previous version 1.13.2 dated 2018-04-27

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of Extension Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

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Package snakecase updated to version 0.9.2 with previous version 0.9.1 dated 2018-03-25

Title: Convert Strings into any Case
Description: A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.
Author: Malte Grosser [aut, cre]
Maintainer: Malte Grosser <malte.grosser@gmail.com>

Diff between snakecase versions 0.9.1 dated 2018-03-25 and 0.9.2 dated 2018-08-14

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Package Rdistance updated to version 2.1.1 with previous version 1.3.2 dated 2015-07-22

Title: Analyses for Distance-Sampling and Abundance Estimation
Description: Distance-sampling is a popular method for abundance estimation in ecology. This package contains functions and associated routines to analyze distance-sampling data collected on point or line transects. It accommodates line and point transect analyses in one routine that accepts a regression-like formula object. Abundance routines perform automated bootstrapping and automated detection-function selection. Overall (study area) and site-level (transect or point) abundance estimates are available. A large suite of classical, parametric detection functions are included. Some uncommon (e.g., Gamma, negative exponential) detection functions are also included and users can define their own custom detection functions if needed. One form of non-parametric smoothed distance function is included. The help files and vignettes have been vetted by multiple authors and tested in multiple workshop settings.
Author: c( person("Trent", "McDonald", email="tmcdonald@west-inc.com", role=c("cre","aut")), person("Ryan", "Nielson", email="rnielson@west-inc.com", role=c("aut")), person("Jason", "Carlisle", email="jcarlisle@west-inc.com", role=c("aut")), person("Aidan", "McDonald", email="aidan@mcdcentral.org", role=c("aut")), person("Ben", "Augustine", email="", role=c("ctb")), person("James", "Griswald", email="", role=c("ctb")), person("Joel", "Reynolds", email="", role=c("ctb")), person("Pham", "Quang", email="", role=c("ctb")), person("Earl", "Becker", email="", role=c("ctb")), person("Aaron", "Christ", email="", role=c("ctb")), person("Brook", "Russelland", email="", role=c("ctb")), person("Patrick", "McKann", email="", role=c("ctb")), person("Lacey", "Jeroue", email="", role=c("ctb")), person("Hoffman", "Abigail", email="", role=c("ctb")), person("Kleinsausser", "Michael", email="", role=c("ctb")) )
Maintainer: Trent McDonald <tmcdonald@west-inc.com>

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More information about Rdistance at CRAN
Permanent link

Package landscapemetrics updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-11

Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>) and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Laura J. Graham [ctb] (<https://orcid.org/0000-0002-1057-3721>), Kimberly A. With [ctb] (<https://orcid.org/0000-0001-5570-1515>), Jeffrey Hollister [ctb] (<https://orcid.org/0000-0002-3611-7281>), Jeremy VanDerWal [ctb] (Original author of underlying C code for get_patches() function), Florian Privé [ctb] (Original author of underlying C++ code for get_nearestneighbour() function)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>

Diff between landscapemetrics versions 0.1.0 dated 2018-08-11 and 0.1.1 dated 2018-08-14

 DESCRIPTION                                    |    7 
 MD5                                            |  102 ++---
 NAMESPACE                                      |    1 
 NEWS.md                                        |    6 
 R/data.R                                       |  330 ++++++++---------
 R/get_adjacencies.R                            |    2 
 R/get_circumscribingcircle.R                   |  136 +++----
 R/get_nearestneighbour.R                       |  158 ++++----
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 R/landscapemetrics-package.R                   |  118 +++---
 R/lsm_c_contig_mn.R                            |  230 ++++++------
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 R/lsm_c_iji.R                                  |  248 ++++++-------
 R/lsm_c_te.R                                   |    4 
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 R/lsm_l_pr.R                                   |  158 ++++----
 R/lsm_l_rpr.R                                  |    4 
 R/lsm_p_core.R                                 |   11 
 R/lsm_p_ncore.R                                |   12 
 R/lsm_p_perim.R                                |    2 
 R/pad_raster.R                                 |   35 +
 R/show_correlation.R                           |  476 ++++++++++++-------------
 inst/doc/getstarted.Rmd                        |  296 +++++++--------
 inst/doc/getstarted.html                       |   18 
 man/lsm_l_rpr.Rd                               |    3 
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 src/get_adjacency.cpp                          |    2 
 tests/testthat/test-calculate-metrics.R        |   64 +--
 tests/testthat/test-get-adjacencies.R          |   60 +--
 tests/testthat/test-get-circumscribungcircle.R |   40 +-
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 tests/testthat/test-get-patches.R              |   32 -
 tests/testthat/test-lsm-c-contig-cv.R          |   82 ++--
 tests/testthat/test-lsm-c-enn-cv.R             |   78 ++--
 tests/testthat/test-lsm-c-frac-cv.R            |   84 ++--
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 tests/testthat/test-show-correlation.R         |   42 +-
 tests/testthat/test-show-patches.R             |   14 
 vignettes/getstarted.Rmd                       |  296 +++++++--------
 52 files changed, 2448 insertions(+), 2413 deletions(-)

More information about landscapemetrics at CRAN
Permanent link

Package phreeqc updated to version 3.4.8 with previous version 3.3.10 dated 2017-01-28

Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh, R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>

Diff between phreeqc versions 3.3.10 dated 2017-01-28 and 3.4.8 dated 2018-08-14

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More information about phreeqc at CRAN
Permanent link

Package geonapi updated to version 0.2-0 with previous version 0.1-0 dated 2018-04-27

Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and exposte it to OGC CSW.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Diff between geonapi versions 0.1-0 dated 2018-04-27 and 0.2-0 dated 2018-08-14

 DESCRIPTION                     |    8 ++--
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More information about geonapi at CRAN
Permanent link

Package rpsftm updated to version 1.2.3 with previous version 1.2.2 dated 2018-01-25

Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of vignette), Annabel Allison [aut] (primary author of vignette, secondary author of code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>

Diff between rpsftm versions 1.2.2 dated 2018-01-25 and 1.2.3 dated 2018-08-14

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 NEWS.md                                                           |    4 
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More information about rpsftm at CRAN
Permanent link

Package XGR updated to version 1.1.4 with previous version 1.1.3 dated 2018-04-13

Title: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between XGR versions 1.1.3 dated 2018-04-13 and 1.1.4 dated 2018-08-14

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More information about XGR at CRAN
Permanent link

Package usethis updated to version 1.4.0 with previous version 1.3.0 dated 2018-02-24

Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Jennifer Bryan [aut] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between usethis versions 1.3.0 dated 2018-02-24 and 1.4.0 dated 2018-08-14

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Package ipred updated to version 0.9-7 with previous version 0.9-6 dated 2017-03-01

Title: Improved Predictors
Description: Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.
Author: Andrea Peters [aut], Torsten Hothorn [aut, cre], Brian D. Ripley [ctb], Terry Therneau [ctb], Beth Atkinson [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package BootValidation updated to version 0.1.65 with previous version 0.1.5 dated 2018-05-18

Title: Adjusting for Optimism in 'glmnet' Regression using Bootstrapping
Description: Main objective of a predictive model is to provide accurated predictions of a new observations. Unfortunately we don't know how well the model performs. In addition, at the current era of omic data where p >> n, is not reasonable applying internal validation using data-splitting. Under this background a good method to assessing model performance is applying internal bootstrap validation (Harrell Jr, Frank E (2015) <doi:10.1007/978-1-4757-3462-1>.) This package provides bootstrap validation for the linear, logistic, multinomial and cox 'glmnet' models as well as lm and glm models.
Author: Antonio Jose Canada Martinez
Maintainer: Antonio Jose Canada Martinez <ancamar2@gmail.com>

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Package BalancedSampling updated to version 1.5.3 with previous version 1.5.2 dated 2016-07-04

Title: Balanced and Spatially Balanced Sampling
Description: Select balanced and spatially balanced probability samples in multi-dimensional spaces with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of the included sampling methods. The local pivotal method and spatially correlated Poisson sampling (for spatially balanced sampling) are included. Also the cube method (for balanced sampling) and the local cube method (for doubly balanced sampling) are included.
Author: Anton Grafström, Jonathan Lisic
Maintainer: Anton Grafström <anton.grafstrom@gmail.com>

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Package DescTools updated to version 0.99.25 with previous version 0.99.24 dated 2018-03-19

Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Andreas Alfons, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Kamil Barton, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Romain Francois, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Christopher Jackson, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Henric Nilsson, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Nathan Russell, Nick Sabbe, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Karline Soetaert, Werner A. Stahel, Alec Stephenson, Mark Stevenson, Matthias Templ, Terry Therneau, Yves Tille, Adrian Trapletti, Joshua Ulrich, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Hadley Wickham, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>

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Package AMR updated to version 0.3.0 with previous version 0.2.0 dated 2018-05-06

Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR) of microbial isolates, by using new S3 classes and applying EUCAST expert rules on antibiograms according to Leclercq (2013) <doi:10.1111/j.1469-0691.2011.03703.x>.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, rev] (<https://orcid.org/0000-0001-5809-5995>), Erwin E.A. Hassing [ctb], Corinna Glasner [ths] (<https://orcid.org/0000-0003-1241-1328>), Alex W. Friedrich [ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu Sinha [ths] (<https://orcid.org/0000-0003-1634-0010>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

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Package ProFit updated to version 1.2.3 with previous version 1.2.1 dated 2018-08-03

Title: Fit Projected 2D Profiles to Galaxy Images
Description: Get data / Define model / ??? / Profit! 'ProFit' is a Bayesian galaxy fitting tool that uses a fast 'C++' image generation library and a flexible interface to a large number of likelihood samplers.
Author: Aaron Robotham, Dan Taranu, Rodrigo Tobar
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>

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Package MANOVA.RM updated to version 0.3.1 with previous version 0.2.1 dated 2017-09-29

Title: Analysis of Multivariate Data and Repeated Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures and general MANOVA designs that do neither assume multivariate normality nor covariance homogeneity, i.e., the procedures are applicable for a wide range of general multivariate factorial designs. Furthermore, post-hoc comparisons are provided for the multivariate analyses. Friedrich, S., Konietschke, F. and Pauly, M. (2018) <arXiv:1801.08002>.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@alumni.uni-ulm.de>

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Package aphid updated to version 1.2.0 with previous version 1.1.0 dated 2018-03-16

Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>

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Package powerlmm updated to version 0.4.0 with previous version 0.3.0 dated 2018-04-17

Title: Power Analysis for Longitudinal Multilevel Models
Description: Calculate power for the 'time x treatment' effect in two- and three-level multilevel longitudinal studies with missing data. Both the third-level factor (e.g. therapists, schools, or physicians), and the second-level factor (e.g. subjects), can be assigned random slopes. Studies with partially nested designs, unequal cluster sizes, unequal allocation to treatment arms, and different dropout patterns per treatment are supported. For all designs power can be calculated both analytically and via simulations. The analytical calculations extends the method described in Galbraith et al. (2002) <doi:10.1016/S0197-2456(02)00205-2>, to three-level models. Additionally, the simulation tools provides flexible ways to investigate bias, Type I errors and the consequences of model misspecification.
Author: Kristoffer Magnusson [aut, cre]
Maintainer: Kristoffer Magnusson <hello@kristoffer.email>

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Package LMfilteR updated to version 0.1.2 with previous version 0.1.1 dated 2017-10-12

Title: Filter Methods for Parameter Estimation in Linear Regression Models
Description: We present a method based on filtering algorithms to estimate the parameters of linear regressions, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods.
Author: Christian Llano Robayo [aut, cre], Nazrul Shaikh [aut]
Maintainer: Christian Llano Robayo <cxl985@miami.edu>

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Package cobalt updated to version 3.4.0 with previous version 3.3.0 dated 2018-06-24

Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with longitudinal treatments.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>

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Mon, 13 Aug 2018

Package togglr updated to version 0.1.33 with previous version 0.1.3 dated 2017-12-07

Title: 'Toggl.com' Api for 'Rstudio'
Description: Use the <http://toggl.com> time tracker api through R.
Author: Vincent Guyader [aut, cre], ThinkR [cph, fnd]
Maintainer: Vincent Guyader <vincent@thinkr.fr>

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Package SpaDES.core updated to version 0.2.2 with previous version 0.2.1 dated 2018-08-09

Title: Core Utilities for Developing and Running Spatially Explicit Discrete Event Simulation Models
Description: Provide the core discrete event simulation (DES) framework for implementing spatially explicit simulation models. The core DES components facilitate modularity, and easily enable the user to include additional functionality by running user-built simulation modules.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>), Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>), Yong Luo [ctb], Steve Cumming [ctb], Ceres Barros [ctb], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>

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Package CSFA updated to version 1.2.0 with previous version 1.1.0 dated 2018-06-13

Title: Connectivity Scores with Factor Analysis
Description: Applies factor analysis methodology to microarray data in order to derive connectivity scores between compounds. The package also contains an implementation of the connectivity score algorithm by Zhang and Gant (2008) <doi:10.1186/1471-2105-9-258>.
Author: Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>

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Package arrangements updated to version 1.1.0 with previous version 1.0.3 dated 2018-08-05

Title: Fast Generators and Iterators for Permutations, Combinations and Partitions
Description: Fast generators and iterators for permutations, combinations and partitions. The iterators allow users to generate arrangements in a memory efficient manner and the generated arrangements are in lexicographical (dictionary) order. Permutations and combinations can be drawn with/without replacement and support multisets. It has been demonstrated that 'arrangements' outperforms most of the existing packages of similar kind. Some benchmarks could be found at <https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package rpart.plot updated to version 3.0.4 with previous version 3.0.3 dated 2018-08-06

Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package IsoplotR updated to version 1.4 with previous version 1.3 dated 2018-06-04

Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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Package GetLattesData updated to version 1.0 with previous version 0.9 dated 2017-11-28

Title: Reading Bibliometric Data from Lattes Platform
Description: A simple API for downloading and reading xml data directly from Lattes <http://lattes.cnpq.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package econet updated to version 0.1.7 with previous version 0.1.6 dated 2018-07-05

Title: Estimation of Parameter-Dependent Network Centrality Measures
Description: Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018), which examine the determinants of US campaign contributions when legislators care about the behavior of other legislators to whom they are socially connected. For additional details, see the vignette.
Author: Marco Battaglini [aut] (<https://orcid.org/0000-0001-9690-0721>), Valerio Leone Sciabolazza [aut, cre] (<https://orcid.org/0000-0003-2537-3084>), Eleonora Patacchini [aut] (<https://orcid.org/0000-0002-3510-2969>), Sida Peng [aut] (<https://orcid.org/0000-0002-2151-0523>)
Maintainer: Valerio Leone Sciabolazza <valerio.leonesciabolazza@uniparthenope.it>

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Package bcp updated to version 4.0.3 with previous version 4.0.2 dated 2018-06-08

Title: Bayesian Analysis of Change Point Problems
Description: Provides an implementation of the Barry and Hartigan (1993) product partition model for the normal errors change point problem using Markov Chain Monte Carlo. It also extends the methodology to regression models on a connected graph (Wang and Emerson, 2015); this allows estimation of change point models with multivariate responses. Parallel MCMC, previously available in bcp v.3.0.0, is currently not implemented.
Author: Xiaofei Wang, Chandra Erdman, and John W. Emerson
Maintainer: Xiaofei Wang <xiaofei.wang@yale.edu>

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Package kirby21.t1 updated to version 1.7.0 with previous version 1.6.0 dated 2018-02-01

Title: Example T1 Structural Data from the Multi-Modal MRI 'Reproducibility' Resource
Description: Structural T1 magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package kirby21.fmri updated to version 1.7.0 with previous version 1.6.0 dated 2018-02-01

Title: Example Functional Imaging Data from the Multi-Modal MRI 'Reproducibility' Resource
Description: Functional magnetic resonance imaging ('fMRI') data from the 'Kirby21' 'reproducibility' study <doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package boostmtree updated to version 1.3.0 with previous version 1.2.1 dated 2018-02-12

Title: Boosted Multivariate Trees for Longitudinal Data
Description: Implements Friedman's gradient descent boosting algorithm for longitudinal data using multivariate tree base learners. A time-covariate interaction effect is modeled using penalized B-splines (P-splines) with estimated adaptive smoothing parameter.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Amol Pande <amoljpande@gmail.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

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Package MFPCA updated to version 1.3 with previous version 1.2-3 dated 2018-07-03

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 (2018) <arXiv:1707.02129>.
Author: Clara Happ [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>

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Package nestfs updated to version 0.8.6 with previous version 0.8.5 dated 2018-08-02

Title: Cross-Validated (Nested) Forward Selection
Description: Implementation of forward selection based on cross-validated linear and logistic regression.
Author: Marco Colombo [aut, cre] (<https://orcid.org/0000-0001-6672-0623>), Felix Agakov [ctb]
Maintainer: Marco Colombo <m.colombo@ed.ac.uk>

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Package matlabr updated to version 1.5.2 with previous version 1.5.0 dated 2018-02-01

Title: An Interface for MATLAB using System Calls
Description: Provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to 'R.matlab', which creates a MATLAB server.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package bigreadr updated to version 0.1.3 with previous version 0.1.0 dated 2018-07-30

Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>

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Package sequoia updated to version 1.1.1 with previous version 1.0.2 dated 2018-04-01

Title: Pedigree Inference from SNPs
Description: Fast multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See citation('sequoia') for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>

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Package kirby21.base updated to version 1.7.0 with previous version 1.6.0 dated 2017-10-11

Title: Example Data from the Multi-Modal MRI 'Reproducibility' Resource
Description: Multi-modal magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <https://www.nitrc.org/projects/multimodal/>, including functional and structural imaging.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package Rspotify updated to version 0.1.2 with previous version 0.1.0 dated 2018-08-07

Title: Access to Spotify API
Description: Provides an interface to the Spotify API <https://developer.spotify.com/documentation/web-api/>.
Author: Tiago Mendes Dantas
Maintainer: Tiago Mendes Dantas <t.mendesdantas@gmail.com>

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Package grplasso updated to version 0.4-6 with previous version 0.4-5 dated 2015-01-23

Title: Fitting User-Specified Models with Group Lasso Penalty
Description: Fits user-specified (GLM-) models with group lasso penalty.
Author: Lukas Meier
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>

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Package gmvarkit updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-28

Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Maximum likelihood estimation of Gaussian Mixture Vector Autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics, forecasting and simulations. Applying general linear constraints to the autoregressive parameters is supported. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>

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Package fansi updated to version 0.3.0 with previous version 0.2.3 dated 2018-05-06

Title: ANSI Control Sequence Aware String Functions
Description: Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.
Author: Brodie Gaslam [aut, cre], Elliott Sales De Andrade [ctb], R Core Team [cph] (UTF8 byte length calcs from src/util.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>

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Package junctions updated to version 1.1 with previous version 1.0.1 dated 2018-04-17

Title: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Description: Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018) <doi:10.1101/058107>.
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>

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Package GENEAclassify updated to version 1.4.14 with previous version 1.4.13 dated 2018-08-02

Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut], Aimee Gott [aut], Joss Langford [aut], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>

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Package Brobdingnag updated to version 1.2-6 with previous version 1.2-5 dated 2018-03-18

Title: Very Large Numbers in R
Description: Handles very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. The package includes a vignette that gives a step-by-step introduction to using S4 methods.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package SimInf updated to version 6.1.0 with previous version 6.0.0 dated 2018-04-20

Title: A Framework for Data-Driven Stochastic Disease Spread Simulations
Description: Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>), Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>), Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>), Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>), Attractive Chaos [cph] (Author of 'kvec.h', a generic dynamic array)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

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Package RNeXML updated to version 2.1.2 with previous version 2.1.1 dated 2018-05-07

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>), Kseniia Shumelchyk [aut], Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package onewaytests updated to version 1.8 with previous version 1.7 dated 2018-06-04

Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs, pairwise comparisons, graphical approaches, assesses variance homogeneity and normality of data in each group via tests and plots.
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

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Package RQGIS updated to version 1.0.4 with previous version 1.0.3 dated 2018-01-23

Title: Integrating R with QGIS
Description: Establishes an interface between R and 'QGIS', i.e. it allows the user to access 'QGIS' functionalities from the R console. It achieves this by using the 'QGIS' Python API via the command line. Hence, RQGIS extends R's statistical power by the incredible vast geo-functionality of 'QGIS' (including also 'GDAL', 'SAGA'- and 'GRASS'-GIS among other third-party providers). This in turn creates a powerful environment for advanced and innovative (geo-)statistical geocomputing. 'QGIS' is licensed under GPL version 2 or greater and is available from <http://www.qgis.org/en/site/>.
Author: Jannes Muenchow [aut, cre] (<https://orcid.org/0000-0001-7834-4717>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Jannes Muenchow <jannes.muenchow@uni-jena.de>

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Package netgwas updated to version 1.7.0 with previous version 1.5.0 dated 2018-05-16

Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <arXiv:1710.01063>. NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>

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Package funHDDC updated to version 2.1.0 with previous version 2.0 dated 2018-04-18

Title: Univariate and Multivariate Model-Based Clustering in Group-Specific Functional Subspaces
Description: The funHDDC algorithm (Schmutz et al., 2017) allows to cluster functional univariate or multivariate data by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>

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Package EL2Surv updated to version 1.1 with previous version 1.0 dated 2017-06-28

Title: Empirical Likelihood (EL) for Comparing Two Survival Functions
Description: Functions for computing critical values and implementing the one-sided/two-sided EL tests.
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>

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Package cgraph updated to version 2.0.1 with previous version 2.0.0 dated 2018-08-05

Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various functions including basic arithmetic, trigonometry functions, and linear algebra functions. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>

Diff between cgraph versions 2.0.0 dated 2018-08-05 and 2.0.1 dated 2018-08-13

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Package subprocess updated to version 0.8.3 with previous version 0.8.2 dated 2017-10-22

Title: Manage Sub-Processes in R
Description: Create and handle multiple sub-processes in R, exchange data over standard input and output streams, control their life cycle.
Author: Lukasz Bartnik [aut, cre]
Maintainer: Lukasz Bartnik <l.bartnik@gmail.com>

Diff between subprocess versions 0.8.2 dated 2017-10-22 and 0.8.3 dated 2018-08-13

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Package mets updated to version 1.2.4 with previous version 1.2.3.1 dated 2018-04-30

Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Also contains two-stage binomial modelling that can do pairwise odds-ratio dependence modelling based marginal logistic regression models. This is an alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>

Diff between mets versions 1.2.3.1 dated 2018-04-30 and 1.2.4 dated 2018-08-13

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Package respirometry updated to version 0.7.0 with previous version 0.6.0 dated 2018-01-24

Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct respirometry experiments. Strong emphasis is on aquatic respirometry. Tools focus on helping the researcher setup and conduct experiments. Analysis of the resulting data is not a focus since analyses are often specific to a particular setup, and thus are better created by the researcher individually. This package provides tools for intermittent, flow-through, and closed respirometry techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>

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Sun, 12 Aug 2018

Package PSCBS updated to version 0.64.0 with previous version 0.63.0 dated 2017-06-28

Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package gbutils updated to version 0.3-0 with previous version 0.2-1 dated 2017-10-05

Title: Simulation of Real and Complex Numbers and Small Programming Utilities
Description: Simulate real and complex numbers from distributions of their magnitude and arguments. Optionally, the magnitudes and/or arguments may be fixed in almost arbitrary ways. Plot density and distribution functions with automatic selection of suitable regions. Small programming utilities: check if an object is identical to NA, count positional arguments in a call, set intersection of more than two sets, check if an argument is unnamed, compute the graph of S4 classes in packages.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between gbutils versions 0.2-1 dated 2017-10-05 and 0.3-0 dated 2018-08-12

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Package RagGrid updated to version 0.2.0 with previous version 0.1.1 dated 2018-06-12

Title: A Wrapper of the 'JavaScript' Library 'agGrid'
Description: Data objects in 'R' can be rendered as 'HTML' tables using the 'JavaScript' library 'ag-grid' (typically via 'R Markdown' or 'Shiny'). The 'ag-grid' library has been included in this 'R' package. The package name 'RagGrid' is an abbreviation of 'R agGrid'.
Author: Srikkanth M [aut, cre], Praveen N [aut, ctb]
Maintainer: Srikkanth M <srikkanth18@gmail.com>

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Package jmvcore updated to version 0.9.2.0 with previous version 0.9.1.10 dated 2018-07-28

Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>

Diff between jmvcore versions 0.9.1.10 dated 2018-07-28 and 0.9.2.0 dated 2018-08-12

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Package mirt updated to version 1.29 with previous version 1.28 dated 2018-05-19

Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using unidimensional and multidimensional latent trait models under the Item Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>). Exploratory and confirmatory models can be estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier analyses are available for modeling item testlets. Multiple group analysis and mixed effects designs also are available for detecting differential item and test functioning as well as modeling item and person covariates. Finally, latent class models such as the DINA, DINO, multidimensional latent class, and several other discrete latent variable models, including mixture and zero-inflated response models, are supported.
Author: Phil Chalmers [aut, cre, cph], Joshua Pritikin [ctb], Alexander Robitzsch [ctb], Mateusz Zoltak [ctb], KwonHyun Kim [ctb], Carl F. Falk [ctb], Adam Meade [ctb], Lennart Schneider [ctb], David King [ctb], Chen-Wei Liu [ctb], Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Package maditr updated to version 0.6.0 with previous version 0.5.2 dated 2018-07-18

Title: Pipe-Style Interface for 'data.table'
Description: Package provides pipe-style interface for 'data.table'. It preserves all 'data.table' features without significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data manipulation tasks. For example, you can write 'mtcars %>% take(mean(mpg), by = am)' for aggregation or 'mtcars %>% let(hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional aggregation/modification. 'query_if' function translates its arguments one-to-one to '[.data.table' method. Additionally there are some conveniences such as automatic 'data.frame' conversion to 'data.table'.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>

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Package jmv updated to version 0.9.2.0 with previous version 0.8.6.2 dated 2018-04-06

Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives, t-tests, ANOVAs, regression, correlation matrices, proportion tests, contingency tables, and factor analysis. This package is also useable from the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>

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Sat, 11 Aug 2018

Package clusrank updated to version 0.6-2 with previous version 0.6-1 dated 2018-07-15

Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre], Mei-Ling Ting Lee [ctb], Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>

Diff between clusrank versions 0.6-1 dated 2018-07-15 and 0.6-2 dated 2018-08-11

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Package energy updated to version 1.7-5 with previous version 1.7-4 dated 2018-05-27

Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, k-groups and hierarchical clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.
Author: Maria Rizzo [aut, cre], Gabor Szekely [aut]
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>

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Package chorrrds updated to version 0.1.7 with previous version 0.1.4 dated 2018-04-22

Title: Music Chords Extraction
Description: Extracts music chords from the 'CifraClub' website <https://www.cifraclub.com.br/>. The package also has functions for cleaning the extracted data and feature extraction.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>

Diff between chorrrds versions 0.1.4 dated 2018-04-22 and 0.1.7 dated 2018-08-11

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Package roll updated to version 1.1.1 with previous version 1.0.7 dated 2017-05-01

Title: Rolling Statistics
Description: Fast and efficient computation of rolling statistics for time-series data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>

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Package ceterisParibus updated to version 0.3.0 with previous version 0.2.1 dated 2018-07-05

Title: Ceteris Paribus Profiles
Description: Ceteris Paribus Profiles (What-If Plots) are designed to present model responses around selected points in a feature space. For example around a single prediction for an interesting observation. Plots are designed to work in a model-agnostic fashion, they are working for any predictive Machine Learning model and allow for model comparisons. Ceteris Paribus Plots supplement the Break Down Plots from 'breakDown' package.
Author: Przemyslaw Biecek [aut, cre]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

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Package jmvconnect updated to version 1.0.4 with previous version 1.0.3 dated 2018-07-26

Title: Connect to the 'jamovi' Statistical Spreadsheet
Description: Methods to access data sets from the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information) from R.
Author: Jonathon Love [aut, cre]
Maintainer: Jonathon Love <jon@thon.cc>

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Package sjlabelled updated to version 1.0.13 with previous version 1.0.12 dated 2018-07-08

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package ggeffects updated to version 0.5.0 with previous version 0.4.0 dated 2018-07-03

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects at the mean or average marginal effects from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are ggpredict() and ggaverage(), however, there are some convenient wrapper-functions especially for polynomials or interactions. There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package testthis updated to version 1.0.4 with previous version 1.0.3 dated 2018-01-06

Title: Utils and 'RStudio' Addins to Make Testing Even More Fun
Description: Utility functions and 'RStudio' addins to ease the life of people using 'testthat', 'devtools' and 'usethis' in their package development workflow. Hotkeyable addins are provided for such common tasks as switching between a source file and an associated test file, or running unit tests in a single file. 'testthis' also provides utility function to manage and run tests in subdirectories of the test/testthat directory.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>

Diff between testthis versions 1.0.3 dated 2018-01-06 and 1.0.4 dated 2018-08-11

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Package SuperLearner updated to version 2.0-24 with previous version 2.0-23 dated 2018-03-12

Title: Super Learner Prediction
Description: Implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.
Author: Eric Polley [aut, cre], Erin LeDell [aut], Chris Kennedy [aut], Sam Lendle [ctb], Mark van der Laan [aut, ths]
Maintainer: Eric Polley <polley.eric@mayo.edu>

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Package nsapi updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-06

Title: Connect to the NS (Dutch Railways) API
Description: Access the NS api and download current departure times, disruptions and engineering work, the station list, and travel recommendations from station to station. All results will be returned as a 'data.frame'. NS (Nederlandse Spoorwegen; Dutch Railways) is the largest train travel provider in the Netherlands. for more information about the API itself see <https://www.ns.nl/en/travel-information/ns-api>. To use the API, and this package, you will need to obtain a username and password. More information about authentication and the use of the functions are described in the vignette.
Author: Roel M. Hogervorst [cre, aut] (<https://orcid.org/0000-0001-7509-0328>)
Maintainer: Roel M. Hogervorst <hogervorst.rm@gmail.com>

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Package EcoNetGen updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-17

Title: Simulate and Sample from Ecological Interaction Networks
Description: Randomly generate a wide range of interaction networks with specified size, average degree, modularity, and topological structure. Sample nodes and links from within simulated networks randomly, by degree, by module, or by abundance. Simulations and sampling routines are implemented in 'FORTRAN', providing efficient generation times even for large networks. Basic visualization methods also included. Algorithms implemented here are described in de Aguiar et al. (2017) <arXiv:1708.01242>.
Author: Marcus de Aguiar [aut, cph] (<https://orcid.org/0000-0003-1379-7568>), Erica Newman [aut] (<https://orcid.org/0000-0001-6433-8594>), Mathias Pires [aut] (<https://orcid.org/0000-0003-2500-4748>), NIMBioS [fnd], Carl Boettiger [aut, cre] (<https://orcid.org/0000-0003-4580-091X>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package mosaic updated to version 1.4.0 with previous version 1.3.0 dated 2018-06-30

Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim [aut, cre], Daniel T. Kaplan [aut], Nicholas J. Horton [aut]
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Package lessR updated to version 3.7.6 with previous version 3.7.5 dated 2018-06-03

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package glm2 updated to version 1.2.1 with previous version 1.2 dated 2018-05-25

Title: Fitting Generalized Linear Models
Description: Fits generalized linear models using the same model specification as glm in the stats package, but with a modified default fitting method that provides greater stability for models that may fail to converge using glm.
Author: Ian Marschner [aut] (using code from glm and glm.fit in the stats package), Mark W. Donoghoe [cre, ctb]
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

Diff between glm2 versions 1.2 dated 2018-05-25 and 1.2.1 dated 2018-08-11

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Fri, 10 Aug 2018

Package MAINT.Data updated to version 1.2.3 with previous version 1.2.2 dated 2018-06-30

Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal and Skew-Normal distributions, considering appropriate parameterizations of the variance-covariance matrix that takes into account the intrinsic nature of interval data, and lead to four different possible configuration structures. The Skew-Normal parameters can be estimated by maximum likelihood, while Normal parameters may be estimated by maximum likelihood or robust trimmed maximum likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>

Diff between MAINT.Data versions 1.2.2 dated 2018-06-30 and 1.2.3 dated 2018-08-10

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Package tesseract updated to version 2.3 with previous version 2.2 dated 2018-07-10

Title: Open Source OCR Engine
Description: Bindings to 'Tesseract' <https://opensource.google.com/projects/tesseract>: a powerful optical character recognition (OCR) engine that supports over 100 languages. The engine is highly configurable in order to tune the detection algorithms and obtain the best possible results.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package RSNNS updated to version 0.4-11 with previous version 0.4-10.1 dated 2018-08-10

Title: Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the 'RSNNS' low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir [aut, cre, cph], José M. Benítez [ths], Andreas Zell [ctb] (Part of original SNNS development team), Niels Mache [ctb] (Part of original SNNS development team), Günter Mamier [ctb] (Part of original SNNS development team), Michael Vogt [ctb] (Part of original SNNS development team), Sven Döring [ctb] (Part of original SNNS development team), Ralf Hübner [ctb] (Part of original SNNS development team), Kai-Uwe Herrmann [ctb] (Part of original SNNS development team), Tobias Soyez [ctb] (Part of original SNNS development team), Michael Schmalzl [ctb] (Part of original SNNS development team), Tilman Sommer [ctb] (Part of original SNNS development team), Artemis Hatzigeorgiou [ctb] (Part of original SNNS development team), Dietmar Posselt [ctb] (Part of original SNNS development team), Tobias Schreiner [ctb] (Part of original SNNS development team), Bernward Kett [ctb] (Part of original SNNS development team), Martin Reczko [ctb] (Part of original SNNS external contributors), Martin Riedmiller [ctb] (Part of original SNNS external contributors), Mark Seemann [ctb] (Part of original SNNS external contributors), Marcus Ritt [ctb] (Part of original SNNS external contributors), Jamie DeCoster [ctb] (Part of original SNNS external contributors), Jochen Biedermann [ctb] (Part of original SNNS external contributors), Joachim Danz [ctb] (Part of original SNNS development team), Christian Wehrfritz [ctb] (Part of original SNNS development team), Patrick Kursawe [ctb] (Contributors to SNNS Version 4.3), Andre El-Ama [ctb] (Contributors to SNNS Version 4.3)
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>

Diff between RSNNS versions 0.4-10.1 dated 2018-08-10 and 0.4-11 dated 2018-08-10

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Package RcppCWB updated to version 0.2.5 with previous version 0.2.4 dated 2018-06-15

Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/ Licenses/GPL-3>). The 'CWB' relies on 'pcre' (BSD license, see <https://www.pcre.org/ licence.txt>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en. html>). See the file LICENSE.note for further information. The package includes modified code of the 'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre], Bernard Desgraupes [aut], Sylvain Loiseau [aut], Oliver Christ [ctb], Bruno Maximilian Schulze [ctb], Stefan Evert [ctb], Arne Fitschen [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

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Package nonlinearTseries updated to version 0.2.4 with previous version 0.2.3 dated 2015-07-25

Title: Nonlinear Time Series Analysis
Description: Functions for nonlinear time series analysis. This package permits the computation of the most-used nonlinear statistics/algorithms including generalized correlation dimension, information dimension, largest Lyapunov exponent, sample entropy and Recurrence Quantification Analysis (RQA), among others. Basic routines for surrogate data testing are also included. Part of this work was based on the book "Nonlinear time series analysis" by Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Author: Constantino A. Garcia [aut, cre], Gunther Sawitzki [ctb]
Maintainer: Constantino A. Garcia <constantino.garciama@ceu.es>

Diff between nonlinearTseries versions 0.2.3 dated 2015-07-25 and 0.2.4 dated 2018-08-10

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Package kernlab updated to version 0.9-27 with previous version 0.9-26 dated 2018-04-30

Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre], Alex Smola [aut], Kurt Hornik [aut], National ICT Australia (NICTA) [cph], Michael A. Maniscalco [ctb, cph], Choon Hui Teo [ctb]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>

Diff between kernlab versions 0.9-26 dated 2018-04-30 and 0.9-27 dated 2018-08-10

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Package ModelMetrics updated to version 1.2.0 with previous version 1.1.0 dated 2016-08-26

Title: Rapid Calculation of Model Metrics
Description: Collection of metrics for evaluating models written in C++ using 'Rcpp'.
Author: Tyler Hunt [aut, cre]
Maintainer: Tyler Hunt <thunt@snapfinance.com>

Diff between ModelMetrics versions 1.1.0 dated 2016-08-26 and 1.2.0 dated 2018-08-10

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Package lava updated to version 1.6.3 with previous version 1.6.2 dated 2018-07-02

Title: Latent Variable Models
Description: A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (two-stage)... The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.
Author: Klaus K. Holst [aut, cre], Brice Ozenne [ctb], Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>

Diff between lava versions 1.6.2 dated 2018-07-02 and 1.6.3 dated 2018-08-10

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Package atlas updated to version 1.0.0 with previous version 0.6.0 dated 2018-06-01

Title: Stanford 'ATLAS' Search Engine API
Description: Stanford 'ATLAS' (Advanced Temporal Search Engine) is a powerful tool that allows constructing cohorts of patients extremely quickly and efficiently. This package is designed to interface directly with an instance of 'ATLAS' search engine and facilitates API queries and data dumps. Prerequisite is a good knowledge of the temporal language to be able to efficiently construct a query. More information available at <https://shahlab.stanford.edu/start>.
Author: Vladimir Polony
Maintainer: Vladimir Polony <podalv@gmail.com>

Diff between atlas versions 0.6.0 dated 2018-06-01 and 1.0.0 dated 2018-08-10

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Package RQuantLib updated to version 0.4.5 with previous version 0.4.4 dated 2017-11-08

Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R The 'QuantLib' project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (2009-2010), Terry Leitch (since 2016)
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RQuantLib versions 0.4.4 dated 2017-11-08 and 0.4.5 dated 2018-08-10

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Package dnet updated to version 1.1.4 with previous version 1.1.3 dated 2018-02-23

Title: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology
Description: The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between dnet versions 1.1.3 dated 2018-02-23 and 1.1.4 dated 2018-08-10

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Package BGGE updated to version 0.6.5 with previous version 0.6.4 dated 2018-07-23

Title: Bayesian Genomic Linear Models Applied to GE Genome Selection
Description: Application of genome prediction for a continuous variable, focused on genotype by environment (GE) genomic selection models (GS). It consists a group of functions that help to create regression kernels for some GE genomic models proposed by Jarquín et al. (2014) <doi:10.1007/s00122-013-2243-1> and Lopez-Cruz et al. (2015) <doi:10.1534/g3.114.016097>. Also, it computes genomic predictions based on Bayesian approaches. The prediction function uses an orthogonal transformation of the data and specific priors present by Cuevas et al. (2014) <doi:10.1534/g3.114.013094>.
Author: Italo Granato [aut, cre], Luna-Vázquez Francisco J. [aut], Cuevas Jaime [aut]
Maintainer: Italo Granato <italo.granato@gmail.com>

Diff between BGGE versions 0.6.4 dated 2018-07-23 and 0.6.5 dated 2018-08-10

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Package XML updated to version 3.98-1.15 with previous version 3.98-1.14 dated 2018-08-09

Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: ORPHANED

Diff between XML versions 3.98-1.14 dated 2018-08-09 and 3.98-1.15 dated 2018-08-10

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Package imp4p updated to version 0.7 with previous version 0.6 dated 2018-06-27

Title: Imputation for Proteomics
Description: Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
Author: Quentin Giai Gianetto
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>

Diff between imp4p versions 0.6 dated 2018-06-27 and 0.7 dated 2018-08-10

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Package genBaRcode updated to version 1.1.0 with previous version 1.0.0 dated 2017-09-21

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 1.0.0 dated 2017-09-21 and 1.1.0 dated 2018-08-10

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Package MCMCprecision updated to version 0.3.9 with previous version 0.3.8 dated 2018-04-08

Title: Precision of Discrete Parameters in Transdimensional MCMC
Description: Estimates the precision of transdimensional Markov chain Monte Carlo (MCMC) output, which is often used for Bayesian analysis of models with different dimensionality (e.g., model selection). Transdimensional MCMC (e.g., reversible jump MCMC) relies on sampling a discrete model-indicator variable to estimate the posterior model probabilities. If only few switches occur between the models, precision may be low and assessment based on the assumption of independent samples misleading. Based on the observed transition matrix of the indicator variable, the method of Heck, Overstall, Gronau, & Wagenmakers (2018, Statistics & Computing) <doi:10.1007/s11222-018-9828-0> draws posterior samples of the stationary distribution to (a) assess the uncertainty in the estimated posterior model probabilities and (b) estimate the effective sample size of the MCMC output.
Author: Daniel W. Heck [aut, cre]
Maintainer: Daniel W. Heck <heck@uni-mannheim.de>

Diff between MCMCprecision versions 0.3.8 dated 2018-04-08 and 0.3.9 dated 2018-08-10

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Package libstableR updated to version 1.0.2 with previous version 1.0.1 dated 2018-08-05

Title: Fast and Accurate Evaluation, Random Number Generation and Parameter Estimation of Skew Stable Distributions
Description: Tools for fast and accurate evaluation of skew stable distributions (CDF, PDF and quantile functions), random number generation and parameter estimation.
Author: Javier Royuela del Val [aut, cre], Federico Simmross-Wattenberg [aut], Carlos Alberola López [aut], Bob Rudis [ctb] (Several bugs fixed and added macOS compatibility), Bruce Swihart [ctb] (Several bugs fixed and added macOS compatibility)
Maintainer: Javier Royuela del Val <jroyval@lpi.tel.uva.es>

Diff between libstableR versions 1.0.1 dated 2018-08-05 and 1.0.2 dated 2018-08-10

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Package RcmdrPlugin.SCDA updated to version 1.1.1 with previous version 1.1 dated 2015-01-27

Title: Rcmdr Plugin for Designing and Analyzing Single-Case Experiments
Description: Provides a GUI for the SCVA, SCRT and SCMA packages as described in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>. The package is written as an Rcmdr plugin.
Author: Isis Bulte and Patrick Onghena
Maintainer: Tamal Kumar De <tamalkumar.de@kuleuven.be>

Diff between RcmdrPlugin.SCDA versions 1.1 dated 2015-01-27 and 1.1.1 dated 2018-08-10

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Package ps updated to version 1.1.0 with previous version 1.0.0 dated 2018-07-22

Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut], Dave Daeschler [aut], Giampaolo Rodola' [aut], Gábor Csárdi [aut, cre], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between ps versions 1.0.0 dated 2018-07-22 and 1.1.0 dated 2018-08-10

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Package BrailleR updated to version 0.29.1 with previous version 0.28.0 dated 2018-06-05

Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Debra Warren [aut], Donal Fitzpatrick [ctb], Duncan Murdoch [ctb], Greg Snow [ctb], Henrik Bengtsson [ctb], James Curtis [ctb], JooYoung Seo [ctb], Marshall Flax [ctb], Paul Murrell [aut], Timothy Bilton [aut], Tony Hirst [ctb], Tsan-Kuang Lee [ctb], Volker Sorge [aut], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>

Diff between BrailleR versions 0.28.0 dated 2018-06-05 and 0.29.1 dated 2018-08-10

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Package abn updated to version 1.2 with previous version 1.0.2 dated 2016-11-09

Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <http://www.r-inla.org>. A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website.
Author: Gilles Kratzer [aut, cre] (<https://orcid.org/0000-0002-5929-8935>), Fraser Ian Lewis [aut], Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>), Marta Pittavino [ctb] (<https://orcid.org/0000-0002-1232-1034>)
Maintainer: Gilles Kratzer <gilles.kratzer@math.uzh.ch>

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Package spGARCH updated to version 0.1.6 with previous version 0.1.5 dated 2018-06-29

Title: Spatial ARCH and GARCH Models (spGARCH)
Description: A collection of functions to deal with spatial and spatiotemporal autoregressive conditional heteroscedasticity (spatial ARCH and GARCH models) by Otto, Schmid, Garthoff (2018, Spatial Statistics) <arXiv:1609.00711>: simulation of spatial ARCH-type processes (spARCH, exponential spARCH, complex spARCH); quasi-maximum-likelihood estimation of the parameters of spARCH models and spatial autoregressive models with spARCH disturbances, diagnostic checks, visualizations.
Author: Philipp Otto [cre, aut] (<https://orcid.org/0000-0002-9796-6682>)
Maintainer: Philipp Otto <potto@europa-uni.de>

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Package photobiologyInOut updated to version 0.4.15 with previous version 0.4.14 dated 2018-04-03

Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package mirtCAT updated to version 1.7.1 with previous version 1.7 dated 2018-03-11

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package (Chalmers (2016) <doi:10.18637/jss.v071.i05>). Suitable for applying unidimensional and multidimensional computerized adaptive tests (CAT) using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R. Additionally, optimal test designs (e.g., "shadow testing") are supported for tests which contain a large number of item selection constraints. Finally, package contains tools useful for performing Monte Carlo simulations for studying the behavior of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Package SnakeCharmR updated to version 1.0.7.1 with previous version 1.0.7 dated 2017-10-07

Title: R and Python Integration
Description: Run 'Python' code, make function calls, assign and retrieve variables, etc. from R. A fork from 'rPython' which uses 'jsonlite', 'Rcpp' and has several fixes and improvements.
Author: Alexandre Sieira, forked off of rPython by Carlos J. Gil Bellosta
Maintainer: Alexandre Sieira <alexandre.sieira@gmail.com>

Diff between SnakeCharmR versions 1.0.7 dated 2017-10-07 and 1.0.7.1 dated 2018-08-10

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Package smoothSurv updated to version 2.0.1 with previous version 2.0 dated 2017-09-24

Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: ORPHANED

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Package RSNNS updated to version 0.4-10.1 with previous version 0.4-10 dated 2017-12-10

Title: Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the 'RSNNS' low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir [aut, cre, cph], José M. Benítez [ths], Andreas Zell [ctb] (Part of original SNNS development team), Niels Mache [ctb] (Part of original SNNS development team), Günter Mamier [ctb] (Part of original SNNS development team), Michael Vogt [ctb] (Part of original SNNS development team), Sven Döring [ctb] (Part of original SNNS development team), Ralf Hübner [ctb] (Part of original SNNS development team), Kai-Uwe Herrmann [ctb] (Part of original SNNS development team), Tobias Soyez [ctb] (Part of original SNNS development team), Michael Schmalzl [ctb] (Part of original SNNS development team), Tilman Sommer [ctb] (Part of original SNNS development team), Artemis Hatzigeorgiou [ctb] (Part of original SNNS development team), Dietmar Posselt [ctb] (Part of original SNNS development team), Tobias Schreiner [ctb] (Part of original SNNS development team), Bernward Kett [ctb] (Part of original SNNS development team), Martin Reczko [ctb] (Part of original SNNS external contributors), Martin Riedmiller [ctb] (Part of original SNNS external contributors), Mark Seemann [ctb] (Part of original SNNS external contributors), Marcus Ritt [ctb] (Part of original SNNS external contributors), Jamie DeCoster [ctb] (Part of original SNNS external contributors), Jochen Biedermann [ctb] (Part of original SNNS external contributors), Joachim Danz [ctb] (Part of original SNNS development team), Christian Wehrfritz [ctb] (Part of original SNNS development team), Patrick Kursawe [ctb] (Contributors to SNNS Version 4.3), Andre El-Ama [ctb] (Contributors to SNNS Version 4.3)
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>

Diff between RSNNS versions 0.4-10 dated 2017-12-10 and 0.4-10.1 dated 2018-08-10

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Package RANN.L1 updated to version 2.5.1 with previous version 2.5 dated 2015-05-04

Title: Fast Nearest Neighbour Search (Wraps ANN Library) Using L1 Metric
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L1 (Manhattan, taxicab) metric. Please see package 'RANN' for the same functionality using the L2 (Euclidean) metric.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis, Kirill Müller
Maintainer: ORPHANED

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Package FNN updated to version 1.1.2.1 with previous version 1.1.2 dated 2018-08-02

Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford (cover tree library), Sunil Arya and David Mount (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li
Maintainer: ORPHANED

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Package pubh updated to version 0.4.1 with previous version 0.3.0 dated 2018-07-11

Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand lattice plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre], Deepayan Sarkar [ctb], Mark Stevenson [ctb], Simon Firestone [ctb], Cord Heuer [ctb], Jim Robison-Cox [ctb], Frank Harell [ctb], John Fox [ctb], Kazuki Yoshida [ctb], Tomas Aragon [ctb], Johan Larsson [ctb], R-Core [ctb]
Maintainer: Josie Athens <josie.athens@otago.ac.nz>

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Thu, 09 Aug 2018

Package vinereg updated to version 0.5.0 with previous version 0.3.0 dated 2018-06-02

Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with parametric or nonparametric pair-copulas. See Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and Schallhorn et al. (2017) <arXiv:1705.08310>.
Author: Thomas Nagler [aut, cre], Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>

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More information about vinereg at CRAN
Permanent link

Package vimp updated to version 1.1.0 with previous version 1.0.0 dated 2018-06-24

Title: Nonparametric Variable Importance
Description: Calculate point estimates of and valid confidence intervals for nonparametric variable importance measures in high and low dimensions, using flexible estimators of the underlying regression functions. For more information about the methods, please see Williamson et al. (2017) <https://biostats.bepress.com/uwbiostat/paper422/>.
Author: Brian D. Williamson [aut, cre], Noah Simon [aut], Marco Carone [aut]
Maintainer: Brian D. Williamson <brianw26@uw.edu>

Diff between vimp versions 1.0.0 dated 2018-06-24 and 1.1.0 dated 2018-08-09

 DESCRIPTION                        |    6 -
 MD5                                |    8 -
 R/cv_vim.R                         |   47 +++++----
 inst/doc/introduction_to_vimp.html |  188 ++++++++++++++++++-------------------
 man/cv_vim.Rd                      |   17 ++-
 5 files changed, 142 insertions(+), 124 deletions(-)

More information about vimp at CRAN
Permanent link

Package socialmixr updated to version 0.1.3 with previous version 0.1.2 dated 2018-02-22

Title: Social Mixing Matrices for Infectious Disease Modelling
Description: Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.
Author: Sebastian Funk [aut, cre]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>

Diff between socialmixr versions 0.1.2 dated 2018-02-22 and 0.1.3 dated 2018-08-09

 DESCRIPTION                  |    8 -
 MD5                          |   29 ++--
 NAMESPACE                    |    1 
 NEWS.md                      |    8 +
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More information about socialmixr at CRAN
Permanent link

Package SpaDES.core updated to version 0.2.1 with previous version 0.2.0 dated 2018-07-10

Title: Core Utilities for Developing and Running Spatially Explicit Discrete Event Simulation Models
Description: Provide the core discrete event simulation (DES) framework for implementing spatially explicit simulation models. The core DES components facilitate modularity, and easily enable the user to include additional functionality by running user-built simulation modules.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>), Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>), Yong Luo [ctb], Steve Cumming [ctb], Ceres Barros [ctb], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>

Diff between SpaDES.core versions 0.2.0 dated 2018-07-10 and 0.2.1 dated 2018-08-09

 SpaDES.core-0.2.0/SpaDES.core/tests/testthat/helper-cleanMessage.R                             |only
 SpaDES.core-0.2.1/SpaDES.core/DESCRIPTION                                                      |   29 
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 SpaDES.core-0.2.1/SpaDES.core/NAMESPACE                                                        |    3 
 SpaDES.core-0.2.1/SpaDES.core/NEWS.md                                                          |   24 
 SpaDES.core-0.2.1/SpaDES.core/R/POM.R                                                          |    5 
 SpaDES.core-0.2.1/SpaDES.core/R/cache.R                                                        |  114 ++
 SpaDES.core-0.2.1/SpaDES.core/R/check.R                                                        |    6 
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 SpaDES.core-0.2.1/SpaDES.core/R/copy.R                                                         |    4 
 SpaDES.core-0.2.1/SpaDES.core/R/downloadData.R                                                 |    6 
 SpaDES.core-0.2.1/SpaDES.core/R/experiment.R                                                   |    2 
 SpaDES.core-0.2.1/SpaDES.core/R/helpers.R                                                      |    8 
 SpaDES.core-0.2.1/SpaDES.core/R/moduleCoverage.R                                               |    2 
 SpaDES.core-0.2.1/SpaDES.core/R/moduleMetadata.R                                               |    3 
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 SpaDES.core-0.2.1/SpaDES.core/R/simList-class.R                                                |    4 
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 SpaDES.core-0.2.1/SpaDES.core/R/spades-core-package.R                                          |    7 
 SpaDES.core-0.2.1/SpaDES.core/R/zzz.R                                                          |   24 
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 SpaDES.core-0.2.1/SpaDES.core/man/POM.Rd                                                       |    4 
 SpaDES.core-0.2.1/SpaDES.core/man/Plot.Rd                                                      |    5 
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 SpaDES.core-0.2.1/SpaDES.core/man/checkObject.Rd                                               |   15 
 SpaDES.core-0.2.1/SpaDES.core/man/checkpoint.Rd                                                |    3 
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 SpaDES.core-0.2.1/SpaDES.core/man/doEvent.Rd                                                   |    2 
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 SpaDES.core-0.2.1/SpaDES.core/man/expectsInput.Rd                                              |    3 
 SpaDES.core-0.2.1/SpaDES.core/man/experiment.Rd                                                |    8 
 SpaDES.core-0.2.1/SpaDES.core/man/findModuleName.Rd                                            |    2 
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 SpaDES.core-0.2.1/SpaDES.core/man/globals.Rd                                                   |    3 
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 SpaDES.core-0.2.1/SpaDES.core/man/ls-method.Rd                                                 |    1 
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 SpaDES.core-0.2.1/SpaDES.core/man/moduleMetadata.Rd                                            |    7 
 SpaDES.core-0.2.1/SpaDES.core/man/newModule.Rd                                                 |    1 
 SpaDES.core-0.2.1/SpaDES.core/man/newModuleCode.Rd                                             |    4 
 SpaDES.core-0.2.1/SpaDES.core/man/newModuleDocumentation.Rd                                    |    7 
 SpaDES.core-0.2.1/SpaDES.core/man/newModuleTests.Rd                                            |    1 
 SpaDES.core-0.2.1/SpaDES.core/man/objSize.simList.Rd                                           |    3 
 SpaDES.core-0.2.1/SpaDES.core/man/objects.Rd                                                   |    2 
 SpaDES.core-0.2.1/SpaDES.core/man/packages.Rd                                                  |    1 
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 SpaDES.core-0.2.1/SpaDES.core/man/params.Rd                                                    |    9 
 SpaDES.core-0.2.1/SpaDES.core/man/parseModule.Rd                                               |   10 
 SpaDES.core-0.2.1/SpaDES.core/man/prepareOutput.Rd                                             |    2 
 SpaDES.core-0.2.1/SpaDES.core/man/progress.Rd                                                  |    3 
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 SpaDES.core-0.2.1/SpaDES.core/man/scheduleEvent.Rd                                             |    2 
 SpaDES.core-0.2.1/SpaDES.core/man/setPaths.Rd                                                  |    1 
 SpaDES.core-0.2.1/SpaDES.core/man/simInit.Rd                                                   |   27 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-accessors-envir.Rd                                   |    2 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-accessors-events.Rd                                  |    4 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-accessors-inout.Rd                                   |    9 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-accessors-modules.Rd                                 |    3 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-accessors-paths.Rd                                   |    6 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-accessors-times.Rd                                   |    6 
 SpaDES.core-0.2.1/SpaDES.core/man/simList-class.Rd                                             |    4 
 SpaDES.core-0.2.1/SpaDES.core/man/spades.Rd                                                    |   15 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/helper-initTests.R                                |only
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-cache.R                                      |  181 ++--
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-checkpoint.R                                 |   45 -
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-downloadData.R                               |   14 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-downloadModule.R                             |   14 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-experiment.R                                 |   22 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-load.R                                       |   40 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-module-deps-methods.R                        |   17 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-module-template.R                            |   27 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-paths.R                                      |   68 -
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-save.R                                       |   37 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-simList.R                                    |  413 +++++-----
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-simulation.R                                 |  149 ---
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-timeunits.R                                  |   23 
 SpaDES.core-0.2.1/SpaDES.core/tests/testthat/test-userSuppliedObjs.R                           |    9 
 SpaDES.core-0.2.1/SpaDES.core/vignettes/ii-modules.Rmd                                         |  144 +--
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More information about SpaDES.core at CRAN
Permanent link

Package mongolite updated to version 2.0 with previous version 1.6 dated 2018-07-02

Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre], MongoDB, Inc [cph] (Bundled mongo-c-driver, see AUTHORS file)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between mongolite versions 1.6 dated 2018-07-02 and 2.0 dated 2018-08-09

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 mongolite-2.0/mongolite/src/mongoc/mongoc-apm.c                          |    9 
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 mongolite-2.0/mongolite/src/mongoc/mongoc-collection.c                   | 1506 +++++---
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Package GNE updated to version 0.99-2 with previous version 0.99-1 dated 2015-07-20

Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria. Optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation. See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

Diff between GNE versions 0.99-1 dated 2015-07-20 and 0.99-2 dated 2018-08-09

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Package funData updated to version 1.3 with previous version 1.2 dated 2018-02-21

Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with utility functions.
Author: Clara Happ [aut, cre]
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>

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Package tm.plugin.mail updated to version 0.2-0 with previous version 0.1 dated 2014-06-11

Title: Text Mining E-Mail Plug-in
Description: A plug-in for the tm text mining framework providing mail handling functionality.
Author: Ingo Feinerer [aut] (<https://orcid.org/0000-0001-7656-8338>), Wolfgang Mauerer [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package uGMAR updated to version 3.0.0 with previous version 2.0.3 dated 2018-07-20

Title: Estimate Univariate Gaussian or Student's t Mixture Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR), Student's t Mixture Autoregressive (StMAR) and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models, quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes. Also general linear constraints and restricting autoregressive parameters to be the same for all regimes are supported. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>, Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>

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Package rvinecopulib updated to version 0.3.0.1.0 with previous version 0.2.8.1.0 dated 2018-05-09

Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine copula modeling based on 'Boost' and 'Eigen'. The 'rvinecopulib' package implements the core features of the popular 'VineCopula' package, in particular inference algorithms for both vine copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker and more modern API, improved performances, especially in high dimensions, nonparametric and multi-parameter families. The 'rvinecopulib' package includes 'vinecopulib' as header-only C++ library (currently version 0.3.0). Thus users do not need to install 'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre], Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>

Diff between rvinecopulib versions 0.2.8.1.0 dated 2018-05-09 and 0.3.0.1.0 dated 2018-08-09

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 rvinecopulib-0.3.0.1.0/rvinecopulib/R/RcppExports.R                                                      |   48 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/R/bicop.R                                                            |   11 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/R/getters.R                                                          |   47 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/R/vinecop.R                                                          |   64 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/R/vinecop_plot.R                                                     |   35 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/man/bicop.Rd                                                         |   12 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/bicop_methods.Rd                                                 |   11 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/getters.Rd                                                       |   21 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/mBICV.Rd                                                         |   38 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/plot.bicop_dist.Rd                                               |    3 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/man/predict_bicop.Rd                                                 |    7 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/predict_vine.Rd                                                  |   10 
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 rvinecopulib-0.3.0.1.0/rvinecopulib/man/vine.Rd                                                          |   28 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/vine_methods.Rd                                                  |   24 
 rvinecopulib-0.3.0.1.0/rvinecopulib/man/vinecop.Rd                                                       |   42 
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Package metaplot updated to version 0.7.1 with previous version 0.7.0 dated 2018-08-09

Title: Data-Driven Diagnostic Plots
Description: Designs plots in terms of core structure. See 'example(metaplot)'. Primary arguments are (unquoted) column names; order and type (numeric or not) dictate the resulting plot. Specify any y variables, x variable, any groups variable, and any conditioning variables to metaplot() to generate density plots, boxplots, mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot() to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide' are honored, producing fully annotated plots with minimal effort. Attribute 'guide' is typically units, but may be encoded() to provide interpretations of categorical values (see '?encode'). Utility unpack() transforms scalar column attributes to row values and pack() does the reverse, supporting tool-neutral storage of metadata along with primary data. The package supports customizable aesthetics such as such as reference lines, unity lines, smooths, log transformation, and linear fits. The user may choose between trellis and ggplot output. Compact syntax and integrated metadata promote workflow scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

Diff between metaplot versions 0.7.0 dated 2018-08-09 and 0.7.1 dated 2018-08-09

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Package enveomics.R updated to version 1.3.2 with previous version 1.3 dated 2018-04-17

Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>

Diff between enveomics.R versions 1.3 dated 2018-04-17 and 1.3.2 dated 2018-08-09

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Package spmoran updated to version 0.1.5 with previous version 0.1.4 dated 2018-05-02

Title: Moran's Eigenvector-Based Spatial Regression Models
Description: Functions for estimating fixed and random effects eigenvector spatial filtering models. For details see Murakami (2018) <arXiv:1703.04467>.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>

Diff between spmoran versions 0.1.4 dated 2018-05-02 and 0.1.5 dated 2018-08-09

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Package reclin updated to version 0.1.1 with previous version 0.1.0 dated 2018-06-06

Title: Record Linkage Toolkit
Description: Functions to assist in performing probabilistic record linkage and deduplication: generating pairs, comparing records, em-algorithm for estimating m- and u-probabilities, forcing one-to-one matching. Can also be used for pre- and post-processing for machine learning methods for record linkage.
Author: Jan van der Laan
Maintainer: Jan van der Laan <r@eoos.dds.nl>

Diff between reclin versions 0.1.0 dated 2018-06-06 and 0.1.1 dated 2018-08-09

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Package bacistool updated to version 0.9.6 with previous version 0.9.5 dated 2018-07-24

Title: Bayesian Classification and Information Sharing (BaCIS) Tool for the Design of Multi-Group Phase II Clinical Trials
Description: Provides the design of multi-group phase II clinical trials with binary outcomes using the hierarchical Bayesian classification and information sharing (BaCIS) model. Subgroups are classified into two clusters on the basis of their outcomes mimicking the hypothesis testing framework. Subsequently, information sharing takes place within subgroups in the same cluster, rather than across all subgroups. This method can be applied to the design and analysis of multi-group clinical trials with binary outcomes.
Author: Nan Chen and J. Jack Lee
Maintainer: Nan Chen <nchen2@mdanderson.org>

Diff between bacistool versions 0.9.5 dated 2018-07-24 and 0.9.6 dated 2018-08-09

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Package tmap updated to version 2.1-1 with previous version 2.1 dated 2018-08-06

Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre], Joel Gombin [ctb], Sebastian Jeworutzki [ctb], Kent Russell [ctb], Richard Zijdeman [ctb], John Clouse [ctb], Robin Lovelace [ctb], Jakub Nowosad [ctb], Jannes Muenchow [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

Diff between tmap versions 2.1 dated 2018-08-06 and 2.1-1 dated 2018-08-09

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Package metaplot updated to version 0.7.0 with previous version 0.4.9 dated 2018-03-31

Title: Data-Driven Diagnostic Plots
Description: Designs plots in terms of core structure. See 'example(metaplot)'. Primary arguments are (unquoted) column names; order and type (numeric or not) dictate the resulting plot. Specify any y variables, x variable, any groups variable, and any conditoning variables to metaplot() to generate density plots, boxplots, mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot() to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide' are honored, producing fully annotated plots with minimal effort. Attribute 'guide' is typically units, but may be encoded() to provide interpretations of categorical values (see '?encode'). Utility unpack() transforms scalar column attributes to row values and pack() does the reverse, supporting tool-neutral storage of metadata along with primary data. The package supports customizable aesthetics such as such as reference lines, unity lines, smooths, log transformation, and linear fits. The user may choose between trellis and ggplot output. Compact syntax and integrated metadata promote workflow scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package dMod updated to version 0.4.2 with previous version 0.4 dated 2017-09-08

Title: Dynamic Modeling and Parameter Estimation in ODE Models
Description: The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>

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Package XML updated to version 3.98-1.14 with previous version 3.98-1.13 dated 2018-08-01

Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: ORPHANED

Diff between XML versions 3.98-1.13 dated 2018-08-01 and 3.98-1.14 dated 2018-08-09

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Package trialr updated to version 0.0.3 with previous version 0.0.2 dated 2018-08-08

Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in 'RStan' and R. Some designs are implemented in R for the first time (e.g. 'EffTox' by Thall and Cook, 2004, <https://biostatistics.mdanderson.org/softwaredownload/SingleSoftware.aspx?Software_Id=2>). Given the emphasis on flexibility in Bayesian analysis, the implementations in a common language and style may serve as a cookbook to encourage the use of Bayesian methods in trials. Compiled 'RStan' models are provided in addition to helper classes and functions to perform simulations and inference on observed trial outcomes. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a published Bayesian design you want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre], Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>

Diff between trialr versions 0.0.2 dated 2018-08-08 and 0.0.3 dated 2018-08-09

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 vignettes/library.bib                                                       |   11 +-
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Package scales updated to version 1.0.0 with previous version 0.5.0 dated 2017-08-24

Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package MDSMap updated to version 1.1 with previous version 1.0 dated 2017-11-29

Title: High Density Genetic Linkage Mapping using Multidimensional Scaling
Description: Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.
Author: Katharine F. Preedy <Katharine.preedy@bioss.ac.uk>, Christine A. Hackett <christine.hackett@bioss.ac.uk>
Maintainer: Bram Boskamp <bram.boskamp@bioss.ac.uk>

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Package jcolors updated to version 0.0.3 with previous version 0.0.2 dated 2018-03-05

Title: Colors Palettes for R and 'ggplot2', Additional Themes for 'ggplot2'
Description: Contains a selection of color palettes and 'ggplot2' themes designed by the package author.
Author: Jared Huling [aut, cre]
Maintainer: Jared Huling <jaredhuling@gmail.com>

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Package PairViz updated to version 1.3.2 with previous version 1.3.1 dated 2018-07-24

Title: Visualization using Graph Traversal
Description: Improving graphics by ameliorating order effects, using Eulerian tours and Hamiltonian decompositions of graphs.
Author: C.B. Hurley and R.W. Oldford
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>

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Package HMDHFDplus updated to version 1.9.1 with previous version 1.1.8 dated 2015-09-20

Title: Read Human Mortality Database and Human Fertility Database Data from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<http://www.fertilitydata.org/>), The Japanese Mortality Database (<http://www.ipss.go.jp/p-toukei/JMD>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre], Carl Boe [aut], Jason Hilton [aut], Josh Goldstein [ctb], Stephen Holzman [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>

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Package VariableScreening updated to version 0.2.0 with previous version 0.1.1 dated 2016-07-28

Title: High-Dimensional Screening for Semiparametric Longitudinal Regression
Description: Implements variable screening techniques for ultra-high dimensional regression settings. Techniques for independent (iid) data, varying-coefficient models, and longitudinal data are implemented. The package currently contains three screen functions: screenIID(), screenLD() and screenVCM(), and six methods for simulating dataset: simulateDCSIS(), simulateLD, simulateMVSIS(), simulateMVSISNY(), simulateSIRS() and simulateVCM(). The package is based on the work of Li-Ping ZHU, Lexin LI, Runze LI, and Li-Xing ZHU (2011) <DOI:10.1198/jasa.2011.tm10563>, Runze LI, Wei ZHONG, & Liping ZHU (2012) <DOI:10.1080/01621459.2012.695654>, Jingyuan LIU, Runze LI, & Rongling WU (2014) <DOI:10.1080/01621459.2013.850086> Hengjian CUI, Runze LI, & Wei ZHONG (2015) <DOI:10.1080/01621459.2014.920256>, and Wanghuan CHU, Runze LI and Matthew REIMHERR (2016) <DOI:10.1214/16-AOAS912>. Special thanks are due to Ling Zhang for providing detailed testing and proposing a method for speed improvement on the simulation of data with AR-1 structure.
Author: Runze Li [aut], Liying Huang [aut, cre], John Dziak [aut]
Maintainer: Liying Huang <lxh37@PSU.EDU>

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Package tm1r updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-31

Title: The Integration Between 'IBM COGNOS TM1' and R
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>

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Package stUPscales updated to version 1.0.3.3 with previous version 1.0.3.2 dated 2018-07-10

Title: Spatio-Temporal Uncertainty Propagation Across Multiple Scales
Description: Integrated environmental modelling requires coupling sub-models at different spatial and temporal scales, thus accounting for change of support procedures (aggregation and disaggregation). We contribute to state-of-the-art open source tools that support uncertainty propagation analysis in temporal and spatio-temporal domains. We implement the tool for uncertainty propagation in environmental modelling, with examples in the urban water domain. The functionalities of the class setup and the methods and functions MC.setup, MC.sim, MC.analysis and Agg.t are contained, which are used for setting up, running and analysing Monte Carlo uncertainty propagation simulations, and for spatio-temporal aggregation. We also implement functionalities to model and predict variables that vary in space and time. stUPscales takes uncertainty characterisation and propagation a step further by including temporal and spatio-temporal auto- and cross-correlation, resulting in more realistic (spatio-)temporal series of environmental variables. Due to its modularity, the package allows the implementation of additional methods and functions for spatio-temporal disaggregation of model inputs and outputs, when linking models across multiple space-time scales.
Author: J.A. Torres-Matallana [aut, cre] U. Leopold [ctb] G.B.M. Heuvelink [ctb]
Maintainer: J.A. Torres-Matallana <arturo.torres@list.lu>

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Package Conigrave updated to version 0.4.1 with previous version 0.4.0 dated 2018-08-03

Title: Flexible Tools for Multiple Imputation
Description: Provides a set of tools that can be used across 'data.frame' and 'imputationList' objects.
Author: James Conigrave
Maintainer: James Conigrave <james.conigrave@gmail.com>

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Package logKDE updated to version 0.3.2 with previous version 0.3.1 dated 2018-07-24

Title: Computing Log-Transformed Kernel Density Estimates for Positive Data
Description: Computes log-transformed kernel density estimates for positive data using a variety of kernels. It follows the methods described in Jones, Nguyen and McLachlan (2018) <doi:10.21105/joss.00870>.
Author: Hien D. Nguyen, Andrew T. Jones, and Geoffrey J. McLachlan
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>

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Package relsurv updated to version 2.2 with previous version 2.1-2 dated 2018-04-05

Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>

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Package lslx updated to version 0.6.3 with previous version 0.6.2 dated 2018-03-05

Title: Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood
Description: Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) with LASSO or minimax concave penalty (MCP).
Author: Po-Hsien Huang [cre, aut], Wen-Hsin Hu [aut]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>

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Package FedData updated to version 2.5.5 with previous version 2.5.4 dated 2018-07-05

Title: Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from seven datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 3, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC); the International Tree Ring Data Bank; and the National Land Cover Database (NLCD).
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>

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Wed, 08 Aug 2018

Package datafsm updated to version 0.2.2 with previous version 0.2.1 dated 2017-10-20

Title: Estimating Finite State Machine Models from Data
Description: Automatic generation of finite state machine models of dynamic decision-making that both have strong predictive power and are interpretable in human terms. We use an efficient model representation and a genetic algorithm-based estimation process to generate simple deterministic approximations that explain most of the structure of complex stochastic processes. We have applied the software to empirical data, and demonstrated it's ability to recover known data-generating processes by simulating data with agent-based models and correctly deriving the underlying decision models for multiple agent models and degrees of stochasticity.
Author: Nay John J. [aut], Gilligan Jonathan M. [cre, aut]
Maintainer: Gilligan Jonathan M. <jonathan.gilligan@vanderbilt.edu>

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Package taxa updated to version 0.3.1 with previous version 0.2.1 dated 2018-05-03

Title: Taxonomic Classes
Description: Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data.
Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Zachary Foster [aut, cre] (<https://orcid.org/0000-0002-5075-0948>)
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>

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Package PRISMAstatement updated to version 1.0.4 with previous version 1.0.3 dated 2018-08-04

Title: Plot Flow Charts According to the "PRISMA" Statement
Description: Plot a PRISMA <http://prisma-statement.org/> flow chart describing the identification, screening, eligibility and inclusion or studies in systematic reviews. PRISMA is an evidence-based minimum set of items for reporting in systematic reviews and meta-analyses. PRISMA focuses on the reporting of reviews evaluating randomized trials, but can also be used as a basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>

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Package iterpc updated to version 0.4.1 with previous version 0.4.0 dated 2018-04-24

Title: Efficient Iterator for Permutations and Combinations
Description: Iterator for generating permutations and combinations. They can be either drawn with or without replacement, or with distinct/ non-distinct items (multiset). The generated sequences are in lexicographical order (dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer being maintained. Users are recommended to switch to 'arrangements'.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package trialr updated to version 0.0.2 with previous version 0.0.1 dated 2017-11-21

Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in 'RStan' and R. Some designs are implemented in R for the first time (e.g. 'EffTox' by Thall and Cook, 2004, <https://biostatistics.mdanderson.org/softwaredownload/SingleSoftware.aspx?Software_Id=2>). Given the emphasis on flexibility in Bayesian analysis, the implementations in a common language and style may serve as a cookbook to encourage the use of Bayesian methods in trials. Compiled 'RStan' models are provided in addition to helper classes and functions to perform simulations and inference on observed trial outcomes. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a published Bayesian design you want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre], Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>

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Package WCE updated to version 1.0.2 with previous version 1.0.1 dated 2018-07-04

Title: Weighted Cumulative Exposure Models
Description: A flexible method for modeling cumulative effects of time-varying exposures, weighted according to their relative proximity in time, and represented by time-dependent covariates. The current implementation estimates the weight function in the Cox proportional hazards model. The function that assigns weights to doses taken in the past is estimated using cubic regression splines.
Author: Marie-Pierre Sylvestre, Marie-Eve Beauchamp, Ryan Patrick Kyle, Michal Abrahamowicz
Maintainer: Marie-Pierre Sylvestre <marie-pierre.sylvestre@umontreal.ca>

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Package skpr updated to version 0.54.3 with previous version 0.53.4 dated 2018-07-13

Title: Design of Experiments Suite: Generate and Evaluate Optimal Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre], George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

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Package dlsem updated to version 2.4 with previous version 2.3 dated 2018-06-08

Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models (Pearl, 2000, Chapter 5) <ISBN:978-0-521-89560-6>, where each factor of the joint probability distribution is a distributed-lag linear regression model (Judge et al., 1985, Chapters 9-10) <ISBN: 978-0-471-89530-5>. DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>

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Package CarletonStats updated to version 2.0 with previous version 1.3 dated 2016-07-19

Title: Functions for Statistics Classes at Carleton College
Description: Includes commands for bootstrapping and permutation tests, a command for created grouped bar plots, and a demo of the quantile-normal plot for data drawn from different distributions.
Author: Laura Chihara
Maintainer: Laura Chihara <lchihara@carleton.edu>

Diff between CarletonStats versions 1.3 dated 2016-07-19 and 2.0 dated 2018-08-08

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Package bWGR updated to version 1.5.4 with previous version 1.5.3 dated 2018-06-07

Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM or Gibbs sampling, with optional sampling techniques and kernel term.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between bWGR versions 1.5.3 dated 2018-06-07 and 1.5.4 dated 2018-08-08

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Package collections updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-30

Title: High Performance Container Data Types
Description: Provides high performance container data types such as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between collections versions 0.1.0 dated 2018-07-30 and 0.1.1 dated 2018-08-08

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Package cOde updated to version 0.4.1 with previous version 0.3 dated 2017-09-07

Title: Automated C Code Generation for 'deSolve', 'bvpSolve' and 'Sundials'
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis. Alternatively to 'deSolve', the Sundials 'CVODES' solver is implemented for computation of model sensitivities.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>

Diff between cOde versions 0.3 dated 2017-09-07 and 0.4.1 dated 2018-08-08

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Package airGRteaching updated to version 0.2.3.2 with previous version 0.2.2.2 dated 2018-03-21

Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre], Laurent Coron [aut], Pierre Brigode [aut], Guillaume Thirel [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>

Diff between airGRteaching versions 0.2.2.2 dated 2018-03-21 and 0.2.3.2 dated 2018-08-08

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Package svars updated to version 1.2.1 with previous version 1.2.0 dated 2018-06-07

Title: Data-Driven Identification of SVAR Models
Description: Implements data-driven identification methods for structural vector autoregressive (SVAR) models. Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>), least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>).
Author: Alexander Lange [aut, cre], Bernhard Dalheimer [aut], Helmut Herwartz [aut], Simone Maxand [aut], Hannes Riebl [ctb]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>

Diff between svars versions 1.2.0 dated 2018-06-07 and 1.2.1 dated 2018-08-08

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Package populationPDXdesign updated to version 1.0.3 with previous version 1.0.2 dated 2018-06-15

Title: Designing Population PDX Studies
Description: Run simulations to assess the impact of various designs features and the underlying biological behaviour on the outcome of a Patient Derived Xenograft (PDX) population study. This project can either be deployed to a server as a 'shiny' app or installed locally as a package and run the app using the command 'populationPDXdesignApp()'.
Author: Maria Luisa Guerriero [aut, cre], Natasha Karp [aut]
Maintainer: Maria Luisa Guerriero <maria.guerriero@astrazeneca.com>

Diff between populationPDXdesign versions 1.0.2 dated 2018-06-15 and 1.0.3 dated 2018-08-08

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Package party updated to version 1.3-1 with previous version 1.3-0 dated 2018-04-20

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available. The methods are described in Hothorn et al. (2006) <doi:10.1198/106186006X133933>, Zeileis et al. (2008) <doi:10.1198/106186008X319331> and Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>), Kurt Hornik [aut], Carolin Strobl [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between party versions 1.3-0 dated 2018-04-20 and 1.3-1 dated 2018-08-08

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Package mdmb updated to version 0.9-43 with previous version 0.8-47 dated 2018-07-09

Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005; <doi:10.1198/016214504000001844>). The regression model can be nonlinear (e.g., interaction effects, quadratic effects or B-spline functions). Multilevel models with missing data in predictors are available for Bayesian estimation. Substantive-model compatible multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between mdmb versions 0.8-47 dated 2018-07-09 and 0.9-43 dated 2018-08-08

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 man/frm.Rd                                |   69 +++++++++++++++++++---
 man/mdmb-package.Rd                       |   12 +--
 man/mdmb_regression.Rd                    |    9 ++
 man/yjt_dist.Rd                           |   47 ++++++++++++---
 src/Makevars                              |    2 
 src/Makevars.win                          |    2 
 src/RcppExports.cpp                       |   44 +++++++++++++-
 src/mdmb_rcpp_linreg.cpp                  |   50 +++++++++++++++-
 src/mdmb_rcpp_linreg.h                    |    8 ++
 src/mdmb_rcpp_yjtreg.cpp                  |   63 ++++++++++++++++++++
 50 files changed, 567 insertions(+), 206 deletions(-)

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Package IDmining updated to version 1.0.5 with previous version 1.0.4 dated 2018-03-21

Title: Intrinsic Dimension for Data Mining
Description: Contains techniques for mining large and high-dimensional data sets by using the concept of Intrinsic Dimension (ID). Here the ID is not necessarily an integer. It is extended to fractal dimensions. And the Morisita estimator is used for the ID estimation, but other tools are included as well.
Author: Jean Golay [aut, cre], Mohamed Laib [aut]
Maintainer: Jean Golay <Jean.Golay@unil.ch>

Diff between IDmining versions 1.0.4 dated 2018-03-21 and 1.0.5 dated 2018-08-08

 DESCRIPTION             |    8 ++++----
 MD5                     |   10 +++++-----
 R/MINDID_FMC.R          |    2 +-
 R/RenDim.R              |    2 +-
 man/IDmining-package.Rd |    2 +-
 man/RenDim.Rd           |    2 +-
 6 files changed, 13 insertions(+), 13 deletions(-)

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Package eplusr updated to version 0.8.3 with previous version 0.8.2 dated 2018-07-22

Title: A Toolkit for Using Whole Building Simulation Program 'EnergyPlus'
Description: A rich toolkit of using the whole building simulation program 'EnergyPlus', 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 <hongyuanjia@cqu.edu.cn>

Diff between eplusr versions 0.8.2 dated 2018-07-22 and 0.8.3 dated 2018-08-08

 DESCRIPTION                      |    8 
 MD5                              |   90 -
 NAMESPACE                        |  216 +-
 NEWS.md                          |   41 
 R/assertions.R                   |  376 ++--
 R/constants.R                    |  118 -
 R/eplusr.R                       |    3 
 R/epw.R                          | 2142 +++++++++++++--------------
 R/format.R                       |   69 
 R/idd.R                          |  947 ++++++------
 R/idd_object.R                   |   82 -
 R/idf.R                          |   88 -
 R/idf_object.R                   |  888 +++++------
 R/impl.R                         |  102 +
 R/install.R                      |  590 +++----
 R/job.R                          | 1269 ++++++++--------
 R/param.R                        |   32 
 R/parse.R                        |    2 
 R/run.R                          |  974 ++++++------
 R/units.R                        | 1966 ++++++++++++-------------
 R/validate.R                     |  816 +++++-----
 R/zzz.R                          |    9 
 README.md                        | 3028 +++++++++++++++++++--------------------
 man/clean_wd.Rd                  |   30 
 man/eplus_job.Rd                 |   48 
 man/eplusr-package.Rd            |   88 -
 man/eplusr_option.Rd             |   90 -
 man/epw.Rd                       |  326 ++--
 man/idd.Rd                       |  289 +--
 man/idd_object.Rd                |  360 ++--
 man/idf.Rd                       |  810 +++++-----
 man/idf_object.Rd                |  485 +++---
 man/install_eplus.Rd             |   75 
 man/job.Rd                       |  261 +--
 man/param.Rd                     |  200 +-
 man/param_job.Rd                 |   46 
 man/read_epw.Rd                  |   44 
 man/read_idf.Rd                  |   56 
 man/run_model.Rd                 |  117 -
 man/use_eplus.Rd                 |  107 -
 man/use_idd.Rd                   |  160 +-
 tests/testthat.R                 |    8 
 tests/testthat/helper-copy.R     |only
 tests/testthat/helper-install.R  |only
 tests/testthat/test_idf.R        |    3 
 tests/testthat/test_idf_object.R |   14 
 tests/testthat/test_job.R        |only
 tests/testthat/test_param.R      |only
 48 files changed, 8848 insertions(+), 8625 deletions(-)

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Tue, 07 Aug 2018

Package rplotengine updated to version 1.0-7 with previous version 1.0-6 dated 2016-11-01

Title: R as a Plotting Engine
Description: Generate basic charts either by custom applications, or from a small script launched from the system console, or within the R console. Two ASCII text files are necessary: (1) The graph parameters file, which name is passed to the function 'rplotengine()'. The user can specify the titles, choose the type of the graph, graph output formats (e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend, whether to show or not a grid at the background, etc. (2) The data to be plotted, which name is specified as a parameter ('data_filename') in the previous file. This data file has a tabulated format, with a single character (e.g. tab) between each column, and a headers line located in the first row. Optionally, the file could include data columns for showing confidence intervals.
Author: Pedro-Pablo Garrido Abenza [aut, cre]
Maintainer: Pedro-Pablo Garrido Abenza <pgarrido@umh.es>

Diff between rplotengine versions 1.0-6 dated 2016-11-01 and 1.0-7 dated 2018-08-07

 DESCRIPTION              |    8 -
 MD5                      |   14 +--
 R/rplotengine.R          |  199 ++++++++++++++++++++++++++++-------------------
 inst/extdata/mydata.txt  |    1 
 inst/extdata/mygraph.arg |    1 
 inst/mydata.txt          |    1 
 inst/mygraph.arg         |    1 
 man/rplotengine.Rd       |   13 ++-
 8 files changed, 145 insertions(+), 93 deletions(-)

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