Mon, 19 Feb 2018

Package PlackettLuce updated to version 0.2-2 with previous version 0.2-1 dated 2017-12-07

Title: Plackett-Luce Models for Rankings
Description: Functions to prepare rankings data and fit the Plackett-Luce model jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce (1959, ISBN:0486441369). The standard Plackett-Luce model is generalized to accommodate ties of any order in the ranking. Partial rankings, in which only a subset of items are ranked in each ranking, are also accommodated in the implementation. Disconnected/weakly connected networks implied by the rankings are handled by adding pseudo-rankings with a hypothetical item. Methods are provided to estimate standard errors or quasi-standard errors for inference as well as to fit Plackett-Luce trees. See the package website or vignette for full details.
Author: Heather Turner [aut, cre], Ioannis Kosmidis [aut], David Firth [aut], Jacob van Etten [ctb]
Maintainer: Heather Turner <ht@heatherturner.net>

Diff between PlackettLuce versions 0.2-1 dated 2017-12-07 and 0.2-2 dated 2018-02-19

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Package xaringan updated to version 0.6 with previous version 0.5 dated 2018-01-29

Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Claus Thorn Ekstrøm [ctb], Dawei Lang [ctb], Garrick Aden-Buie [ctb], Ole Petter Bang [ctb] (CSS in rmarkdown/templates/xaringan/resources/default.css), Patrick Schratz [ctb], Sean Lopp [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between xaringan versions 0.5 dated 2018-01-29 and 0.6 dated 2018-02-19

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Package rgdax updated to version 0.4.0 with previous version 0.3.0 dated 2018-02-18

Title: Wrapper for 'GDAX' Cryptocurrency Exchange
Description: Allow access to both public and private end points to 'GDAX' cryptocurrency exchange. For authenticated flow, users must have valid api, secret and passphrase to be able to connect. Read more details on getting access to 'GDAX' API at: <https://support.gdax.com/customer/en/portal/articles/2425383-how-can-i-create-an-api-key-for-gdax->.
Author: person("Dheeraj", "Agarwal", email = "dheeeraj.agarwal@gmail.com", role = c("aut", "cre"))
Maintainer: Dheeraj Agarwal <dheeeraj.agarwal@gmail.com>

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Package MSCMT updated to version 1.3.2 with previous version 1.3.1 dated 2018-01-04

Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has already an implementation in package 'Synth') are implemented: first, 'MSCMT' allows for using multiple outcome variables, second, time series can be supplied as economic predictors, and third, a well-defined cross-validation approach can be used. Much effort has been taken to make the implementation as stable as possible (including edge cases) without losing computational efficiency. A detailed description of the main algorithms is given in Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] (<https://orcid.org/0000-0003-2336-9751>), Stefan Klößner [aut], Karline Soetaert [com], LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>

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Package tidytext updated to version 0.1.7 with previous version 0.1.6 dated 2018-01-07

Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using 'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb], Oliver Keyes [ctb], David Robinson [aut], Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>

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Package tidyquant updated to version 0.5.4 with previous version 0.5.3 dated 2017-08-03

Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

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More information about tidyquant at CRAN
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Package stringr updated to version 1.3.0 with previous version 1.2.0 dated 2017-02-18

Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.
Author: Hadley Wickham [aut, cre, cph], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package qtl updated to version 1.42-8 with previous version 1.42-7 dated 2018-02-18

Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>

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Package MetaComp updated to version 1.1.1 with previous version 1.0.1 dated 2017-03-02

Title: EDGE Taxonomy Assignments Visualization
Description: Implements routines for metagenome sample taxonomy assignments collection, aggregation, and visualization. Accepts the EDGE-formatted output from GOTTCHA/GOTTCHA2, BWA, Kraken, MetaPhlAn, DIAMOND, and Pangia. Produces SVG and PDF heatmap-like plots comparing taxa abundances across projects.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <senin@hawaii.edu>

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Package forcats updated to version 0.3.0 with previous version 0.2.0 dated 2017-01-23

Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package dbplyr updated to version 1.2.1 with previous version 1.2.0 dated 2018-01-03

Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
Author: Hadley Wickham [aut, cre], Edgar Ruiz [aut], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package colorhcplot updated to version 1.3.1 with previous version 1.0 dated 2015-10-01

Title: Colorful Hierarchical Clustering Dendrograms
Description: Build dendrograms with sample groups highlighted by different colors. Visualize results of hierarchical clustering analyses as dendrograms whose leaves and labels are colored according to sample grouping. Assess whether data point grouping aligns to naturally occurring clusters.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>

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Package archivist updated to version 2.3 with previous version 2.2 dated 2017-11-25

Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut], Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

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Package IROmiss updated to version 1.0.1 with previous version 1.0.0 dated 2018-01-17

Title: Imputation Regularized Optimization Algorithm
Description: Missing data are frequently encountered in high-dimensional data analysis, but they are usually difficult to deal with using standard algorithms, such as the EM algorithm and its variants. This package provides a general algorithm, the so-called Imputation Regularized Optimization (IRO) algorithm, for high-dimensional missing data problems. You can refer to Liang, F., Jia, B., Xue, J., Li, Q. and Luo, Y. (2018) at <arXiv:1802.02251> for detail.
Author: Bochao Jia [aut, ctb, cre, cph], Faming Liang [ctb]
Maintainer: Bochao Jia <jbc409@ufl.edu>

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Package textmineR updated to version 2.1 with previous version 2.0.6 dated 2017-08-17

Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that should be familiar to experienced R users. Provides a wrapper for several topic models that take similarly-formatted input and give similarly-formatted output. Has additional functionality for analyzing and diagnostics for topic models.
Author: Thomas Jones [aut, cre], William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>

Diff between textmineR versions 2.0.6 dated 2017-08-17 and 2.1 dated 2018-02-19

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Package GGIR updated to version 1.5-17 with previous version 1.5-16 dated 2018-01-17

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in van Hees and colleagues (2014) <doi: 10.1152/japplphysiol.00421.2014> and (2015) <doi: 10.1371/journal.pone.0142533>. The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <http://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com/product/ax3>. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb], Jairo H Migueles [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>

Diff between GGIR versions 1.5-16 dated 2018-01-17 and 1.5-17 dated 2018-02-19

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Package archdata updated to version 1.2 with previous version 1.1 dated 2016-04-04

Title: Example Datasets from Archaeological Research
Description: The archdata package provides several types of data that are typically used in archaeological research. It provides all of the data sets used in "Quantitative Methods in Archaeology Using R" by David L Carlson, one of the Cambridge Manuals in Archaeology.
Author: David L. Carlson and Georg Roth
Maintainer: David L. Carlson <dcarlson@tamu.edu>

Diff between archdata versions 1.1 dated 2016-04-04 and 1.2 dated 2018-02-19

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Package fmriqa updated to version 0.3.0 with previous version 0.2.0 dated 2017-12-20

Title: Functional MRI Quality Assurance Routines
Description: Methods for performing fMRI quality assurance (QA) measurements of test objects. Heavily based on the fBIRN procedures detailed by Friedman and Glover (2006) <doi:10.1002/jmri.20583>.
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

Diff between fmriqa versions 0.2.0 dated 2017-12-20 and 0.3.0 dated 2018-02-19

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Package rcompanion updated to version 1.11.3 with previous version 1.11.1 dated 2017-11-12

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>

Diff between rcompanion versions 1.11.1 dated 2017-11-12 and 1.11.3 dated 2018-02-19

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Package clinDR updated to version 1.7 with previous version 1.6 dated 2017-12-04

Title: Simulation and Analysis Tools for Clinical Dose Response Modeling
Description: Bayesian and ML Emax model fitting, graphics and simulation for clinical dose response. The summary data from the dose response meta-analyses in Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229> are included in the package. The prior distributions for the Bayesian analyses default to the posterior predictive distributions derived from these references.
Author: Neal Thomas [aut, cre] (<https://orcid.org/0000-0002-1915-8487>), Jing Wu [aut]
Maintainer: Neal Thomas <snthomas99@gmail.com>

Diff between clinDR versions 1.6 dated 2017-12-04 and 1.7 dated 2018-02-19

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Package bmrm updated to version 3.7 with previous version 3.4 dated 2017-08-16

Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk under L1 or L2 regularization. Implements the algorithm proposed by Teo et al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR 2012). The package comes with lot of loss functions for machine learning which make it powerful for big data analysis. The applications includes: structured prediction, linear SVM, multi-class SVM, f-beta optimization, ROC optimization, ordinal regression, quantile regression, epsilon insensitive regression, least mean square, logistic regression, least absolute deviation regression (see package examples), etc... all with L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados <julien.prados@unige.ch>

Diff between bmrm versions 3.4 dated 2017-08-16 and 3.7 dated 2018-02-19

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New package WMWssp with initial version 0.3.2
Package: WMWssp
Type: Package
Title: Wilcoxon-Mann-Whitney Sample Size Planning
Version: 0.3.2
Date: 2018-02-16
Authors@R: c( person("Arne C. Bathke", role = "aut"), person("Edgar Brunner", role = "aut"), person("Martin Happ", role = c("aut", "cre"), email = "martin.happ@aon.at"), person("Frank Konietschke", role = "aut") )
Author: Arne C. Bathke [aut], Edgar Brunner [aut], Martin Happ [aut, cre], Frank Konietschke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Description: Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test that is needed for a given power and two sided type I error rate. The method works for metric data with and without ties, count data, ordered categorical data, and even dichotomous data. But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect. For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Imports: rankFD
Depends: R (>= 3.4.0)
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 09:56:57 UTC; b1011921
Repository: CRAN
Date/Publication: 2018-02-19 10:24:30 UTC

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New package projpred with initial version 0.7.0
Package: projpred
Title: Projection Predictive Feature Selection
Version: 0.7.0
Author: Markus Paasiniemi [aut], Juho Piironen [aut], Jonah Gabry [ctb], Aki Vehtari [ctb]
Maintainer: Juho Piironen <juho.piironen@aalto.fi>
Description: Performs projection predictive feature selection for generalized linear models (see, e.g., Piironen and Vehtari, 2017, <doi:10.1007/s11222-016-9649-y>). The package is compatible with 'rstanarm' package, but other reference models can also be used. See the package vignette for more information and examples.
Depends: R (>= 3.1.2)
Imports: rstan, rstanarm (>= 2.17.2), loo, ggplot2, Rcpp, utils
LinkingTo: Rcpp, RcppArmadillo
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown, glmnet, bayesplot
VignetteBuilder: knitr
URL: https://github.com/stan-dev/projpred
BugReports: https://github.com/stan-dev/projpred/issues
NeedsCompilation: yes
Packaged: 2018-02-18 19:26:42 UTC; juho
Repository: CRAN
Date/Publication: 2018-02-19 10:10:41 UTC

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New package mfGARCH with initial version 0.1.2
Package: mfGARCH
Title: Mixed-Frequency GARCH Models
Version: 0.1.2
Authors@R: person("Onno", "Kleen", email = "r@onnokleen.de", role = c("aut", "cre"))
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: volatility forecasting using multiplicative component GARCH models" by Conrad, Kleen (2018, Working Paper). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: Rcpp, graphics, stats, numDeriv, zoo
LinkingTo: Rcpp
URL: https://github.com/onnokleen/mfGARCH/
BugReports: https://github.com/onnokleen/mfGARCH/issues
Suggests: testthat, dplyr, ggplot2, covr, rmarkdown
NeedsCompilation: yes
Packaged: 2018-02-19 10:02:58 UTC; Arbeit
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>
Repository: CRAN
Date/Publication: 2018-02-19 10:27:25 UTC

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New package GpGp with initial version 0.1.0
Package: GpGp
Type: Package
Title: Fast Gaussian Process Computation Using Vecchia's Approximation
Version: 0.1.0
Date: 2018-02-18
Authors@R: c( person("Joseph", "Guinness", email = "joeguinness@gmail.com", role = c("aut", "cre")), person("Matthias", "Katzfuss", email = "katzfuss@gmail.com", role = "aut" ) )
Maintainer: Joseph Guinness <joeguinness@gmail.com>
Description: Functions for reordering input locations, finding ordered nearest neighbors (with help from 'FNN' package), grouping operations, approximate likelihood evaluations, profile likelihoods, Gaussian process predictions, and conditional simulations. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. The original approximation is due to Vecchia (1988) <http://www.jstor.org/stable/2345768>, and the reordering and grouping methods are from Guinness (2018) <doi:10.1080/00401706.2018.1437476>.
Depends: R (>= 2.10)
License: MIT + file LICENSE
Imports: Rcpp (>= 0.12.13), FNN
Suggests: fields, knitr, rmarkdown, testthat
LinkingTo: Rcpp
RoxygenNote: 6.0.1
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2018-02-18 21:48:51 UTC; guinness
Author: Joseph Guinness [aut, cre], Matthias Katzfuss [aut]
Repository: CRAN
Date/Publication: 2018-02-19 10:14:03 UTC

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Package funrar updated to version 1.2.1 with previous version 1.2.0 dated 2017-06-30

Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. funrar is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenié [aut, cre] (<https://orcid.org/0000-0002-4659-7522>), Pierre Denelle [aut] (<https://orcid.org/0000-0001-5037-2281>), Caroline Tucker [aut] (<https://orcid.org/0000-0002-4871-2010>), François Munoz [ths] (<https://orcid.org/0000-0001-8776-4705>), Cyrille Violle [ths] (<https://orcid.org/0000-0002-2471-9226>)
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>

Diff between funrar versions 1.2.0 dated 2017-06-30 and 1.2.1 dated 2018-02-19

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Package confSAM updated to version 0.2 with previous version 0.1 dated 2017-01-18

Title: Estimates and Bounds for the False Discovery Proportion, by Permutation
Description: For multiple testing. Computes estimates and confidence bounds for the False Discovery Proportion (FDP), the fraction of false positives among all rejected hypotheses. The methods in the package use permutations of the data. Doing so, they take into account the dependence structure in the data.
Author: Jesse Hemerik and Jelle Goeman
Maintainer: Jesse Hemerik <j.b.a.hemerik@lumc.nl>

Diff between confSAM versions 0.1 dated 2017-01-18 and 0.2 dated 2018-02-19

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Package XML updated to version 3.98-1.10 with previous version 3.98-1.9 dated 2017-06-19

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 3.98-1.9 dated 2017-06-19 and 3.98-1.10 dated 2018-02-19

 DESCRIPTION           |    6 +++---
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New package SPUTNIK with initial version 1.0.0
Package: SPUTNIK
Type: Package
Title: SPatially aUTomatic deNoising for Ims toolKit
Version: 1.0.0
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>
Authors@R: c(person("Paolo", "Inglese", email = "p.inglese14@imperial.ac.uk", role = c("aut", "cre")), person("Goncalo", "Correia", role = c("aut", "ctb")))
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.
Depends: R (>= 3.4.0)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: no
Imports: spatstat, autothresholdr, viridis, viridisLite, SDMTools, ggplot2, reshape, imager, methods, infotheo
RoxygenNote: 6.0.1
URL: https://github.com/paoloinglese/SPUTNIK
BugReports: https://github.com/paoloinglese/SPUTNIK/issues
NeedsCompilation: no
Packaged: 2018-02-16 21:11:56 UTC; pi514
Repository: CRAN
Date/Publication: 2018-02-19 09:17:36 UTC

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New package riskyr with initial version 0.1.0
Package: riskyr
Type: Package
Title: Rendering Risk Literacy more Transparent
Version: 0.1.0
Date: 2018-02-16
Authors@R: c(person("Hansjoerg", "Neth", role = c("aut", "cre"), email = "h.neth@uni.kn"), person("Felix", "Gaisbauer", role = "aut"), person("Nico", "Gradwohl", role = "aut"), person("Wolfgang", "Gaissmaier", role = "aut"))
Author: Hansjoerg Neth [aut, cre], Felix Gaisbauer [aut], Nico Gradwohl [aut], Wolfgang Gaissmaier [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Description: Risk-related information can be expressed in terms of probabilities or frequencies. By providing a toolbox of methods and metrics, we compute, translate, and represent risk-related information in a variety of ways. By offering different, but complementary perspectives on the interplay between key parameters, 'riskyr' renders teaching and training of risk literacy more transparent.
Depends: R (>= 3.2)
Imports: diagram (>= 1.6.4), grid (>= 3.4.3), vcd (>= 1.4), utils (>= 3.4.3)
Suggests: devtools, rmarkdown, knitr, roxygen2
Collate: 'comp_util.R' 'init_txt.R' 'init_pal.R' 'init_prob.R' 'comp_prob_prob.R' 'init_freq.R' 'comp_freq_prob.R' 'init_num.R' 'init_prob_num.R' 'init_freq_num.R' 'comp_freq_freq.R' 'comp_prob_freq.R' 'comp_xxxx_prob.R' 'comp_popu.R' 'comp_accu.R' 'plot_mosaic.R' 'plot_icons.R' 'plot_tree.R' 'plot_fnet.R' 'plot_curve.R' 'plot_plane.R' 'data.R' 'read_data.R' 'riskyr_class.R' 'start_riskyr.R'
Encoding: UTF-8
LazyData: true
License: GPL-2 | GPL-3
BugReports: https://github.com/hneth/riskyr/issues
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 22:34:00 UTC; hneth
Repository: CRAN
Date/Publication: 2018-02-19 09:22:19 UTC

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New package forestControl with initial version 0.1.1
Package: forestControl
Type: Package
Title: Approximate False Positive Rate Control in Selection Frequency for Random Forest
Version: 0.1.1
Date: 2018-02-16
Authors@R: c( person("Tom", "Wilson", , "tpw2@aber.ac.uk", c("aut", "cre")), person("Jasen", "Finch", , "jsf9@aber.ac.uk", "aut"))
Description: Approximate false positive rate control in selection frequency for random forest using the methods described by Ender Konukoglu and Melanie Ganz (2015) <arXiv:1410.2838>. Methods for calculating the selection frequency threshold at false positive rates and selection frequency false positive rate feature selection.
Imports: Rcpp
Suggests: testthat, randomForest, ranger
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/aberHRML/forestControl
BugReports: https://github.com/aberHRML/forestControl/issues
RoxygenNote: 6.0.1
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-02-16 22:06:58 UTC; tom
Author: Tom Wilson [aut, cre], Jasen Finch [aut]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>
Repository: CRAN
Date/Publication: 2018-02-19 09:20:11 UTC

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Sun, 18 Feb 2018

Package SamplingStrata updated to version 1.2 with previous version 1.1 dated 2016-01-13

Title: Optimal Stratification of Sampling Frames for Multipurpose Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Marco Ballin, Daniela Pagliuca, Egon Willighagen, Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>

Diff between SamplingStrata versions 1.1 dated 2016-01-13 and 1.2 dated 2018-02-18

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Package RcppNumerical updated to version 0.3-2 with previous version 0.3-1 dated 2016-12-09

Title: 'Rcpp' Integration for Numerical Computing Libraries
Description: A collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with 'Rcpp'.
Author: Yixuan Qiu [aut, cre], Sreekumar Balan [aut] (Numerical integration library), Matt Beall [aut] (Numerical integration library), Mark Sauder [aut] (Numerical integration library), Naoaki Okazaki [aut] (The libLBFGS library), Thomas Hahn [aut] (The Cuba library)
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

Diff between RcppNumerical versions 0.3-1 dated 2016-12-09 and 0.3-2 dated 2018-02-18

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Package kernelboot updated to version 0.1.4 with previous version 0.1.3 dated 2017-12-18

Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Description: Smoothed bootstrap and functions for random generation from univariate and multivariate kernel densities. It does not estimate kernel densities.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>

Diff between kernelboot versions 0.1.3 dated 2017-12-18 and 0.1.4 dated 2018-02-18

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Package devtools updated to version 1.13.5 with previous version 1.13.4 dated 2017-11-09

Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Jim Hester <james.hester@rstudio.com>

Diff between devtools versions 1.13.4 dated 2017-11-09 and 1.13.5 dated 2018-02-18

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New package agRee with initial version 0.5-1
Package: agRee
Title: Various Methods for Measuring Agreement
Version: 0.5-1
Author: Dai Feng
Description: Bland-Altman plot and scatter plot with identity line for visualization and point and interval estimates for different metrics related to reproducibility/repeatability/agreement including the concordance correlation coefficient, intraclass correlation coefficient, within-subject coefficient of variation, smallest detectable difference, and mean normalized smallest detectable difference.
Maintainer: Dai Feng <dai_feng@merck.com>
Depends: R (>= 3.0.2), miscF (>= 0.1-4), lme4 (>= 1.0-4)
Imports: R2jags (>= 0.03-11), coda (>= 0.16-1)
License: GPL
NeedsCompilation: no
Packaged: 2018-02-18 21:34:49 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-18 21:55:41 UTC

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New package sim1000G with initial version 1.38
Package: sim1000G
Type: Package
Title: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Version: 1.38
Date: 2018-02-16
Author: Apostolos Dimitromanolakis <apostolis@live.ca>, Jingxiong Xu <jingxiong.xu@mail.utoronto.ca>, Agnieszka Krol <krol@lunenfeld.ca>, Laurent Briollais <laurent@lunenfeld.ca>
Maintainer: Apostolos Dimitromanolakis <apostolis@live.ca>
Description: Generates realistic simulated genetic data in families or unrelated individuals.
License: GPL (>= 2)
Depends: R (>= 2.15.2), stats, hapsim, MASS, stringr, readr
NeedsCompilation: no
VignetteBuilder: knitr, prettydoc
RoxygenNote: 6.0.1
Suggests: knitr, prettydoc, testthat, rmarkdown, gplots
Encoding: UTF-8
Repository: CRAN
Packaged: 2018-02-17 17:23:46 UTC; apo
Date/Publication: 2018-02-18 21:30:35 UTC

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Package rgdax updated to version 0.3.0 with previous version 0.2.0 dated 2018-01-09

Title: Wrapper for 'GDAX' Cryptocurrency Exchange
Description: Allow access to both public and private end points to 'GDAX' cryptocurrency exchange. For authenticated flow, users must have valid api, secret and passphrase to be able to connect. Read more details on getting access to 'GDAX' API at: <https://support.gdax.com/customer/en/portal/articles/2425383-how-can-i-create-an-api-key-for-gdax->.
Author: person("Dheeraj", "Agarwal", email = "dheeeraj.agarwal@gmail.com", role = c("aut", "cre"))
Maintainer: Dheeraj Agarwal <dheeeraj.agarwal@gmail.com>

Diff between rgdax versions 0.2.0 dated 2018-01-09 and 0.3.0 dated 2018-02-18

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New package PottsUtils with initial version 0.3-3
Package: PottsUtils
Title: Utility Functions of the Potts Models
Version: 0.3-3
Author: Dai Feng [aut, cre], Luke Tierney [ctb]
Description: There are three sets of functions. The first produces basic properties of a graph and generates samples from multinomial distributions to facilitate the simulation functions (they maybe used for other purposes as well). The second provides various simulation functions for a Potts model in Potts, R. B. (1952) <doi:10.1017/S0305004100027419>. The third currently includes only one function which computes the normalizing constant of a Potts model based on simulation results.
Maintainer: Dai Feng <daifeng.stat@gmail.com>
Depends: R (>= 3.0.2)
Imports: miscF (>= 0.1-4)
License: GPL-2
NeedsCompilation: yes
Packaged: 2018-02-18 20:53:32 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-18 21:04:47 UTC

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New package ecospace with initial version 1.2.3
Package: ecospace
Type: Package
Title: Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks
Version: 1.2.3
Date: 2018-01-17
Depends: R (>= 3.4.0)
Imports: FD (>= 1.0-12)
Authors@R: person("Phil", "Novack-Gottshall", email = "pnovack-gottshall@ben.edu", role = c("aut", "cre"))
Maintainer: Phil Novack-Gottshall <pnovack-gottshall@ben.edu>
Description: Implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.
License: CC0
URL: https://github.com/pnovack-gottshall/ecospace, http://www.ben.edu/faculty/pnovack-gottshall/index.html
LazyData: TRUE
BugReports: https://github.com/pnovack-gottshall/ecospace/issues
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, vegan
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-18 18:28:36 UTC; pnovack-gottshall
Author: Phil Novack-Gottshall [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-18 21:09:27 UTC

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New package codingMatrices with initial version 0.3.2
Package: codingMatrices
Type: Package
Title: Alternative Factor Coding Matrices for Linear Model Formulae
Version: 0.3.2
Author: Bill Venables
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Description: A collection of coding functions as alternatives to the standard functions in the stats package, which have names starting with 'contr.'. Their main advantage is that they provide a consistent method for defining marginal effects in factorial models. In a simple one-way ANOVA model the intercept term is always the simple average of the class means.
Depends: stats
Imports: Matrix, methods, fractional, utils
Suggests: knitr, MASS, dplyr, car, ggplot2, xtable
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-18 21:02:18 UTC; ven037
Repository: CRAN
Date/Publication: 2018-02-18 21:30:34 UTC

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Package binequality updated to version 1.0.3 with previous version 1.0.2 dated 2017-07-09

Title: Methods for Analyzing Binned Income Data
Description: Methods for model selection, model averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation, etc, on binned income data where the topmost bin is right-censored. We provide both a non-parametric method, termed the bounded midpoint estimator (BME), which assigns cases to their bin midpoints; except for the censored bins, where cases are assigned to an income estimated by fitting a Pareto distribution. Because the usual Pareto estimate can be inaccurate or undefined, especially in small samples, we implement a bounded Pareto estimate that yields much better results. We also provide a parametric approach, which fits distributions from the generalized beta (GB) family. Because some GB distributions can have poor fit or undefined estimates, we fit 10 GB-family distributions and use multimodel inference to obtain definite estimates from the best-fitting distributions. We also provide binned income data from all United States of America school districts, counties, and states.
Author: Samuel V. Scarpino, Paul von Hippel, and Igor Holas
Maintainer: Samuel V. Scarpino <s.scarpino@northeastern.edu>

Diff between binequality versions 1.0.2 dated 2017-07-09 and 1.0.3 dated 2018-02-18

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Package tfruns updated to version 1.3 with previous version 1.2 dated 2018-01-18

Title: Training Run Tools for 'TensorFlow'
Description: Create and manage unique directories for each 'TensorFlow' training run. Provides a unique, time stamped directory for each run along with functions to retrieve the directory of the latest run or latest several runs.
Author: JJ Allaire [aut, cre], RStudio [cph, fnd], Mike Bostock [cph] (D3 library - https://d3js.org/), Masayuki Tanaka [cph] (C3 library - http://c3js.org/), jQuery Foundation [cph] (jQuery library), jQuery contributors [cph] (jQuery library; authors: inst/views/components/jquery-AUTHORS.txt), Shaun Bowe [cph] (jQuery visibilityChanged plugin), Materialize [cph] (Materizlize library - https://materializecss.com/), Yuxi You [cph] (Vue.js library - https://vuejs.org/), Kevin Decker [cph] (jsdiff library - https://github.com/kpdecker/jsdiff/), Rodrigo Fernandes [cph] (diff2html library - https://diff2html.xyz/), Ivan Sagalaev [cph] (highlight.js library - https://highlightjs.org/), Yauheni Pakala [cph] (highlightjs-line-numbers library)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between tfruns versions 1.2 dated 2018-01-18 and 1.3 dated 2018-02-18

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Package serrsBayes updated to version 0.3-12 with previous version 0.3-11 dated 2018-02-15

Title: Bayesian Modelling of Raman Spectroscopy
Description: Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS), using the method of Moores et al. (2016) <arXiv:1604.07299>. Multivariate observations of SERRS are highly collinear and lend themselves to a reduced-rank representation. The GAMM separates the SERRS signal into three components: a sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline; and additive white noise. The parameters of each component of the model are estimated iteratively using SMC. The posterior distributions of the parameters given the observed spectra are represented as a population of weighted particles.
Author: Matt Moores [aut, cre] (<https://orcid.org/0000-0003-4531-3572>), Jake Carson [aut], Mark Girolami [aut], Engineering and Physical Sciences Research Council [fnd] (EPSRC programme grant ref: EP/L014165/1), University of Warwick [cph]
Maintainer: Matt Moores <M.T.Moores@warwick.ac.uk>

Diff between serrsBayes versions 0.3-11 dated 2018-02-15 and 0.3-12 dated 2018-02-18

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Package gambin updated to version 2.3.0 with previous version 2.2.0 dated 2017-12-05

Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>. 'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre], Michael Krabbe Borregaard [aut], Karl Ugland [aut], Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>

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Package ratios updated to version 1.2.0 with previous version 1.1.0 dated 2017-07-18

Title: Calculating Ratios Between Two Data Sets and Correction for Adhering Particles on Plants
Description: Calculation of ratios between two data sets containing environmental data like element concentrations by different methods. Additionally plant element concentrations can be corrected for adhering particles (soil, airborne dust).
Author: Solveig Pospiech [aut, cre], Wiebke Fahlbusch [ctb]
Maintainer: Solveig Pospiech <s.pospiech@gmx.de>

Diff between ratios versions 1.1.0 dated 2017-07-18 and 1.2.0 dated 2018-02-18

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Package Phase123 updated to version 1.4 with previous version 1.2 dated 2018-02-07

Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew Chapple <andrew.g.chapple@rice.edu>

Diff between Phase123 versions 1.2 dated 2018-02-07 and 1.4 dated 2018-02-18

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Package likelihoodAsy updated to version 0.50 with previous version 0.45 dated 2016-11-02

Title: Functions for Likelihood Asymptotics
Description: Functions for computing the r and r* statistics for inference on an arbitrary scalar function of model parameters, plus some code for the (modified) profile likelihood.
Author: Ruggero Bellio and Donald Pierce
Maintainer: Ruggero Bellio <ruggero.bellio@uniud.it>

Diff between likelihoodAsy versions 0.45 dated 2016-11-02 and 0.50 dated 2018-02-18

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Package RJafroc updated to version 1.0.1 with previous version 1.0.0 dated 2018-02-04

Title: Modeling, Analysis, Validation and Visualization of Observer Performance Studies in Diagnostic Radiology
Description: Tools for quantitative assessment of medical imaging systems, radiologists or computer aided ('CAD') algorithms. Implements methods described in a book: 'Chakraborty' 'DP' (2017), "Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples", Taylor-Francis <https://www.crcpress.com/9781482214840>. Data collection paradigms include receiver operating characteristic ('ROC') and its location specific extensions, primarily free-response 'ROC' ('FROC'). 'ROC' data consists of a single rating per image, where the rating is the perceived confidence level the image is of a diseased patient. 'FROC' data consists of a variable number (including zero) of mark-rating pairs per image, where a mark is the location of a clinically reportable suspicious region and the rating is the corresponding confidence level that it is a true lesion. The software supersedes the current Windows version of 'JAFROC' software <http://www.devchakraborty.com>. 'RJafroc' is derived from it being an enhanced R version of original Windows 'JAFROC'. Implemented are a number of figures of merit quantifying performance, functions for visualizing operating characteristics; three ROC ratings data curve-fitting algorithms: the 'binormal' model ('BM'), the contaminated binormal model ('CBM') and the radiological search model ('RSM'). Unlike the 'BM', the 'CBM' and the 'RSM' predict proper ROC curves that do not cross the chance diagonal or display inappropriate hooks near the upper right corner of the plots. 'RSM' fitting additionally yields measures of search and lesion-classification performances, in addition to the usual case-classification performance measured by the area under the 'ROC' curve. Search performance is the ability to find lesions while avoiding finding non-lesions. Lesion-classification performance is the ability to discriminate between found lesions and non-lesions. For fully crossed study designs, termed multiple-reader multiple-case, significance testing of reader-averaged figure-of-merit differences between modalities is implemented via both 'Dorfman', 'Berbaum' and 'Metz' ('DBM') and the 'Obuchowski' and 'Rockette' ('OR') methods. Single treatment analysis allows comparison of performance of a group of radiologists to a specified value, or comparison of 'CAD' performance to a group of radiologists interpreting the same cases. Sample size estimation tools are provided for 'ROC' and 'FROC' studies that allow estimation of relevant variances from a pilot study to predict required numbers of readers and cases in a pivotal study. Utility and data file manipulation functions allow data to be read in any of the currently used input formats, including Excel, and the results of the analysis can be viewed in text or Excel output files. The package is used extensively in the online appendices of the cited book. Directions for accessing the online material are available by following the software tab of <http://www.devchakraborty.com>.
Author: Dev Chakraborty [cre, aut, cph], Xuetong Zhai [aut, cph], Lucy D'Agostino McGowan [ctb]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>

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Package imbalance updated to version 1.0.0 with previous version 0.1.1 dated 2017-11-15

Title: Preprocessing Algorithms for Imbalanced Datasets
Description: Class imbalance usually damages the performance of classifiers. Thus, it is important to treat data before applying a classifier algorithm. This package includes recent resampling algorithms in the literature: (Barua et al. 2014) <doi:10.1109/tkde.2012.232>; (Das et al. 2015) <doi:10.1109/tkde.2014.2324567>, (Zhang et al. 2014) <doi:10.1016/j.inffus.2013.12.003>; (Gao et al. 2014) <doi:10.1016/j.neucom.2014.02.006>; (Almogahed et al. 2014) <doi:10.1007/s00500-014-1484-5>. It also includes an useful interface to perform oversampling.
Author: Ignacio Cordón [aut, cre], Salvador García [aut], Alberto Fernández [aut], Francisco Herrera [aut]
Maintainer: Ignacio Cordón <nacho.cordon.castillo@gmail.com>

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Package githubinstall updated to version 0.2.2 with previous version 0.2.1 dated 2016-11-21

Title: A Helpful Way to Install R Packages Hosted on GitHub
Description: Provides an helpful way to install packages hosted on GitHub.
Author: Koji Makiyama [cre, aut], Atsushi Hayakawa [ctb], Shinya Uryu [ctb], Hiroaki Yutani [ctb], Nagi Teramo [ctb], Kazuhiro Maeda [ctb]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>

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Package EpiILM updated to version 1.4.1 with previous version 1.4 dated 2018-02-03

Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar. K. V. and Rob Deardon
Maintainer: Vineetha Warriyar. K. V. <vineethawarriyar.kod@ucalgary.ca>

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Package ECOSolveR updated to version 0.4 with previous version 0.3-2 dated 2017-09-25

Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS), an efficient and robust C library for convex problems. Conic and equality constraints can be specified in addition to integer and boolean variable constraints for mixed-integer problems. This R interface is inspired by the python interface and has similar calling conventions.
Author: Anqi Fu [aut], Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>

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Package tidyLPA updated to version 0.1.2 with previous version 0.1.1 dated 2018-02-14

Title: Easily Carry Out Latent Profile Analysis
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Rebecca R Steingut [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

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Package metamisc updated to version 0.1.8 with previous version 0.1.7 dated 2017-11-20

Title: Diagnostic and Prognostic Meta-Analysis
Description: Meta-analysis of diagnostic and prognostic modeling studies. Summarize estimates of prognostic factors, diagnostic test accuracy and prediction model performance. Validate, update and combine published prediction models. Develop new prediction models with data from multiple studies.
Author: Thomas Debray [aut, cre], Valentijn de Jong [aut]
Maintainer: Thomas Debray <thomas.debray@gmail.com>

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Package bookdown updated to version 0.7 with previous version 0.6 dated 2018-01-25

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Christophe Dervieux [ctb], Clifton Franklund [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Peter Hickey [ctb], Sahir Bhatnagar [ctb], Steve Simpson [ctb], Vincent Fulco [ctb], Yixuan Qiu [ctb], Zhuoer Dong [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

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Package spacyr updated to version 0.9.6 with previous version 0.9.3 dated 2017-11-10

Title: Wrapper to the 'spaCy' 'NLP' Library
Description: An R wrapper to the 'Python' 'spaCy' 'NLP' library, from <http://spacy.io>.
Author: Kenneth Benoit [aut, cre, cph], Akitaka Matsuo [aut]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package qtl updated to version 1.42-7 with previous version 1.41-6 dated 2017-06-12

Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>

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Package WRSS updated to version 1.1 with previous version 1.0 dated 2017-11-09

Title: Water Resources System Simulator
Description: Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems.'WRSS' proposes functions and methods for construction, simulation and analysis of primary water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
Author: Rezgar Arabzadeh; Parisa Aberi; Kaveh Panaghi; Shahab Araghinejad; Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>

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Package biosignalEMG updated to version 2.1.0 with previous version 2.0.2 dated 2018-02-09

Title: Tools for Electromyogram Signals (EMG) Analysis
Description: Data processing tools to compute the rectified, integrated and the averaged EMG. Routines for automatic detection of activation phases. A routine to compute and plot the ensemble average of the EMG. An EMG signal simulator for general purposes.
Author: J.A. Guerrero, J.E. Macias-Diaz
Maintainer: Antonio Guerrero <jaguerrero@correo.uaa.mx>

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Sat, 17 Feb 2018

Package rstanarm updated to version 2.17.3 with previous version 2.17.2 dated 2017-12-21

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Imad Ali [ctb], Sam Brilleman [ctb], Jacqueline Buros Novik [ctb] (R/stan_jm.R), AstraZeneca [ctb] (R/stan_jm.R), Trustees of Columbia University [cph], Simon Wood [cph] (R/stan_gamm4.R), R Core Deveopment Team [cph] (R/stan_aov.R), Douglas Bates [cph] (R/pp_data.R), Martin Maechler [cph] (R/pp_data.R), Ben Bolker [cph] (R/pp_data.R), Steve Walker [cph] (R/pp_data.R), Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R), William Venables [cph] (R/stan_polr.R), Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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Package pryr updated to version 0.1.4 with previous version 0.1.3 dated 2017-10-30

Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the language at a deeper level.
Author: Hadley Wickham [aut, cre], R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package petro.One updated to version 0.1.3 with previous version 0.1.1 dated 2017-11-02

Title: Statistics and Text Mining for Oil and Gas Papers from OnePetro Metadata
Description: Application that retrieves papers metadata from the OnePetro website. Thousands of papers on oil and gas live in OnePetro. By retrieving metadata from the search queries, a summary of papers that match the query words, can be retrieved for further analysis and text mining. There are some statistics and data mining provided such as word cloud plots, keywords frequency, conversion to corpus document, and removal of common usage words. OnePetro link: <https://www.onepetro.org/>.
Author: Alfonso R. Reyes [aut, cre]
Maintainer: Alfonso R. Reyes <alfonso.reyes@oilgainsanalytics.com>

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Package kamila updated to version 0.1.1.2 with previous version 0.1.1.1 dated 2016-08-18

Title: Methods for Clustering Mixed-Type Data
Description: Implements methods for clustering mixed-type data, specifically combinations of continuous and nominal data. Special attention is paid to the often-overlooked problem of equitably balancing the contribution of the continuous and categorical variables. This package implements KAMILA clustering, a novel method for clustering mixed-type data in the spirit of k-means clustering. It does not require dummy coding of variables, and is efficient enough to scale to rather large data sets. Also implemented is Modha-Spangler clustering, which uses a brute-force strategy to maximize the cluster separation simultaneously in the continuous and categorical variables.
Author: Alexander Foss [aut, cre], Marianthi Markatou [aut]
Maintainer: Alexander Foss <alexanderhfoss@gmail.com>

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Package grattan updated to version 1.5.3.5 with previous version 1.5.3.1 dated 2018-01-21

Title: Australian Tax Policy Analysis
Description: Utilities for costing and evaluating Australian tax policy, including high-performance tax and transfer calculators, a fast method of projecting tax collections, and an interface to common indices from the Australian Bureau of Statistics. Written to support Grattan Institute's Australian Perspectives program. For access to the 'taxstats' package, please run install.packages("taxstats", repos = "https://hughparsonage.github.io/drat/", type = "source"). N.B. The 'taxstats' package is approximately 50 MB.
Author: Hugh Parsonage [aut, cre], Tim Cameron [aut], Brendan Coates [aut], William Young [aut], Ittima Cherastidtham [dtc], W. Karsten [ctb], M. Enrique Garcia [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

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Package detrendr updated to version 0.4.0 with previous version 0.2.0 dated 2018-01-04

Title: Detrend Images
Description: Image series affected by bleaching must be corrected by 'detrending' prior to the performance of quantitative analysis. 'detrendr' is for correctly detrending images. It uses Nolan's algorithm (Nolan et al., 2017 <doi:10.1093/bioinformatics/btx434>).
Author: Rory Nolan [aut, cre, cph], Sergi Padilla-Parra [ths, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package CovTools updated to version 0.3.0 with previous version 0.2.1 dated 2017-11-15

Title: Statistical Tools for Covariance Analysis
Description: Covariance is of universal prevalence across various disciplines within statistics. We provide a rich collection of geometric and inferential tools for convenient analysis of covariance structures, topics including distance measures, mean covariance estimator, covariance hypothesis test for one-sample and two-sample cases, and covariance estimation. For an introduction to covariance in multivariate statistical analysis, see Schervish (1987) <doi:10.1214/ss/1177013111>.
Author: Kyoungjae Lee [aut], Lizhen Lin [ctb], Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>

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Package gamlss.spatial updated to version 1.3.5 with previous version 1.3.4 dated 2017-08-10

Title: Spatial Terms in Generalized Additive Models for Location Scale and Shape Models
Description: It allows us to fit Gaussian Markov Random Field within the Generalized Additive Models for Location Scale and Shape algorithms.
Author: Fernanda De Bastiani [aut, cre, cph], Mikis Stasinopoulos [aut], Robert Rigby [aut]
Maintainer: Fernanda De Bastiani <fernandadebastiani@gmail.com>

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Package Compind updated to version 2.0 with previous version 1.2.1 dated 2017-12-07

Title: Composite Indicators Functions
Description: Contains functions to enhance approaches to the Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps.
Author: Francesco Vidoli, Elisa Fusco
Maintainer: Francesco Vidoli <fvidoli@gmail.com>

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Fri, 16 Feb 2018

Package PowerUpR updated to version 0.2.3 with previous version 0.1.3 dated 2017-02-17

Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: R version of PowerUp! <https://www.causalevaluation.org/>. Includes tools to calculate statistical power, minimum detectable effect size, and minimum required sample size for various multilevel randomized experiments with continuous outcomes.
Author: Metin Bulus [aut, cre, trl], Nianbo Dong [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

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New package miscF with initial version 0.1-4
Package: miscF
Title: Miscellaneous Functions
Version: 0.1-4
Author: Dai Feng
Description: Various functions for random number generation, density estimation, classification, curve fitting, and spatial data analysis.
Maintainer: Dai Feng <dai_feng@merck.com>
Depends: R (>= 3.0.2), MASS (>= 7.3-45), R2jags (>= 0.5-7)
Imports: MCMCpack (>= 1.2-4), mvtnorm (>= 0.9-9992)
Suggests: mixAK (>= 2.6), BRugs (>= 0.8-6)
License: GPL
NeedsCompilation: yes
Packaged: 2018-02-16 21:41:16 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-16 22:59:53 UTC

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Package findR updated to version 0.2.0 with previous version 0.1.0 dated 2018-01-30

Title: Find Code Snippets, R Scripts, R Markdown, PDF and Text Files with Pattern Matching
Description: Scans all directories and subdirectories of a path for code snippets, R scripts, R Markdown, PDF or text files containing a specific pattern. Files found can be copied to a new folder.
Author: David Zumbach [aut, cre]
Maintainer: David Zumbach <david.zumbach@gfzb.ch>

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New package spider with initial version 1.5.0
Package: spider
Type: Package
Title: Species Identity and Evolution in R
Version: 1.5.0
Date: 2018-02-15
Author: Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Maintainer: Rupert A. Collins <rupertcollins@gmail.com>
Description: Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.
License: MIT + file LICENSE
LazyLoad: yes
Imports: ape, pegas, graphics, stats, utils
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-02-16 19:05:02 UTC; rc16041
Repository: CRAN
Date/Publication: 2018-02-16 19:33:47 UTC

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Package NNS updated to version 0.3.8.3 with previous version 0.3.8.2 dated 2018-01-08

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

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Package MST updated to version 2.1 with previous version 2.0 dated 2017-04-15

Title: Multivariate Survival Trees
Description: Constructs trees for multivariate survival data using marginal and frailty models. Grows, prunes, and selects the best-sized tree.
Author: Xiaogang Su [aut], Peter Calhoun [aut, cre], Juanjuan Fan [aut]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>

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Package largeVis updated to version 0.2.1.1 with previous version 0.2.1 dated 2017-05-08

Title: High-Quality Visualizations of Large, High-Dimensional Datasets
Description: Implements the largeVis algorithm (see Tang, et al. (2016) <DOI:10.1145/2872427.2883041>) for visualizing very large high-dimensional datasets. Also very fast search for approximate nearest neighbors; outlier detection; and optimized implementations of the HDBSCAN*, DBSCAN and OPTICS clustering algorithms; plotting functions for visualizing the above.
Author: Amos B. Elberg
Maintainer: ORPHANED

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New package dub with initial version 0.1.0
Package: dub
Type: Package
Title: Unpacking Assignment for Lists via Pattern Matching
Version: 0.1.0
Authors@R: person("Eugene", "Ha", , "eha@posteo.de", c("aut", "cre"))
Description: Provides an operator for assigning nested components of a list to names via a concise, Haskell-like pattern matching syntax. This is especially convenient for assigning individual names to the multiple values that a function may return in the form of a list, and for extracting deeply nested list components.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
ByteCompile: true
Suggests: covr, testthat
URL: https://github.com/egnha/dub
BugReports: https://github.com/egnha/dub/issues
Collate: 'util.R' 'assert.R' 'tree.R' 'names.R' 'assign.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 13:40:32 UTC; eha
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Repository: CRAN
Date/Publication: 2018-02-16 19:24:08 UTC

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New package adklakedata with initial version 0.6.1
Package: adklakedata
Type: Package
Title: Adirondack Long-Term Lake Data
Version: 0.6.1
Authors@R: c(person("Luke", "Winslow", role = c("aut", "cre"), email = "lawinslow@gmail.com"), person("Taylor", "Leach", role=c("aut")), person("Tobi", "Hahn", role=c("aut")))
Description: Package for the access and distribution of Long-term lake datasets from lakes in the Adirondack Park, northern New York state. Includes a wide variety of physical, chemical, and biological parameters from 28 lakes. Data are from multiple collection organizations and have been harmonized in both time and space for ease of reuse.
License: MIT + file LICENSE
Imports: rappdirs, httr, tools, utils
Suggests: ggplot2, maps, testthat, sf
Repository: CRAN
BugReports: https://github.com/lawinslow/adklakedata/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 15:34:27 UTC; lawinslow
Author: Luke Winslow [aut, cre], Taylor Leach [aut], Tobi Hahn [aut]
Maintainer: Luke Winslow <lawinslow@gmail.com>
Date/Publication: 2018-02-16 19:08:16 UTC

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Package lfe updated to version 2.6-2291 with previous version 2.5-1998 dated 2016-04-18

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>

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New package IBCF.MTME with initial version 1.1-2
Package: IBCF.MTME
Title: Item Based Collaborative Filtering for Multi-Trait and Multi-Environment Data
Version: 1.1-2
Date: 2018-02-14
Authors@R: c(person("Francisco Javier", "Luna-Vazquez", email = "frahik@gmail.com", role = c("aut", "cre")), person("Osval Antonio", "Montesinos-Lopez", email= "oamontes1@ucol.mx", role = "aut"), person("Abelardo", "Montesinos-Lopez", role = "aut"), person("Jose", "Crossa", role = "aut"))
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>
Description: Implements the Item based collaborative filtering (IBCF) method for continues phenotypes in the context of plant breeding where data are collected for various traits that were studied in various environments proposed by Montesinos-López et al. (2017) <doi:10.1534/g3.117.300309>.
Depends: R (>= 3.0.0)
License: LGPL-3
Encoding: UTF-8
LazyData: true
Type: Package
RoxygenNote: 6.0.1
URL: https://github.com/frahik/IBCF.MTME
BugReports: https://github.com/frahik/IBCF.MTME/issues/new
NeedsCompilation: no
Collate: CrossValidation.R IBCF.R IBCF.MTME.R IBCFYear.R methods.R Td2M.R Title.R Wheat_IBCF.R Year_IBCF.R
Imports: lsa, tidyr
Suggests: testthat, knitr, rmarkdown
Packaged: 2018-02-16 00:59:22 UTC; Francisco
Author: Francisco Javier Luna-Vazquez [aut, cre], Osval Antonio Montesinos-Lopez [aut], Abelardo Montesinos-Lopez [aut], Jose Crossa [aut]
Repository: CRAN
Date/Publication: 2018-02-16 18:29:26 UTC

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New package estudy2 with initial version 0.8.4
Package: estudy2
Type: Package
Title: An Implementation of Parametric and Nonparametric Event Study
Version: 0.8.4
Date: 2018-02-16
Authors@R: person("Iegor", "Rudnytskyi", , "iegor.rudnytskyi@gmail.com", c("aut", "cre"))
Description: An implementation of a most commonly used event study methodology, including both parametric and nonparametric tests. It contains variety aspects of the rate of return estimation (the core calculation is done in C++), as well as three classical for event study market models: mean adjusted returns, market adjusted returns and single-index market models. There are 6 parametric and 6 nonparametric tests provided, which examine cross-sectional daily abnormal return (see the documentation of the functions for more information). Parametric tests include tests proposed by Brown and Warner (1980) <DOI:10.1016/0304-405X(80)90002-1>, Brown and Warner (1985) <DOI:10.1016/0304-405X(85)90042-X>, Boehmer et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Patell (1976) <DOI:10.2307/2490543>, and Lamb (1995) <DOI:10.2307/253695>. Nonparametric tests covered in estudy2 are tests described in Corrado and Zivney (1992) <DOI:10.2307/2331331>, McConnell and Muscarella (1985) <DOI:10.1016/0304-405X(85)90006-6>, Boehmer et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Cowan (1992) <DOI:10.1007/BF00939016>, Corrado (1989) <DOI:10.1016/0304-405X(89)90064-0>, Campbell and Wasley (1993) <DOI:10.1016/0304-405X(93)90025-7>, Savickas (2003) <DOI:10.1111/1475-6803.00052>, Kolari and Pynnonen (2010) <DOI:10.1093/rfs/hhq072>. Furthermore, tests for the cumulative abnormal returns proposed by Brown and Warner (1985) <DOI:10.1016/0304-405X(85)90042-X> and Lamb (1995) <DOI:10.2307/253695> are included.
License: GPL-3
LazyData: TRUE
URL: http://github.com/irudnyts/estudy2
BugReports: http://github.com/irudnyts/estudy2/issues
Depends: R (>= 3.1)
Imports: tseries (>= 0.10-42), zoo (>= 1.8-0), matrixStats (>= 0.52.2), Rcpp (>= 0.12.13)
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, magrittr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-02-16 11:11:19 UTC; irudnyts
Author: Iegor Rudnytskyi [aut, cre]
Maintainer: Iegor Rudnytskyi <iegor.rudnytskyi@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-16 18:32:52 UTC

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Package nlme updated to version 3.1-131.1 with previous version 3.1-135.5 dated 2018-02-16

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>

Diff between nlme versions 3.1-135.5 dated 2018-02-16 and 3.1-131.1 dated 2018-02-16

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Package RSiteCatalyst updated to version 1.4.14 with previous version 1.4.13 dated 2017-07-21

Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4 (<https://api.omniture.com/admin/1.4/rest/>).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>

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Package recurse updated to version 1.1.0 with previous version 1.0.1 dated 2017-12-11

Title: Computes Revisitation Metrics for Trajectory Data
Description: Computes revisitation metrics for trajectory data, such as the number of revisitations for each location as well as the time spent for that visit and the time since the previous visit. Also includes functions to plot data.
Author: Chloe Bracis <cbracis@uw.edu>
Maintainer: Chloe Bracis <cbracis@uw.edu>

Diff between recurse versions 1.0.1 dated 2017-12-11 and 1.1.0 dated 2018-02-16

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More information about recurse at CRAN
Permanent link

New package ppcSpatial with initial version 0.1.0
Package: ppcSpatial
Type: Package
Title: Spatial Analysis of Pakistan Population Census
Version: 0.1.0
Authors@R: c( person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")) , person(c("Muhammad", "Arfan", "Dilber"), email = "pbsfsd041@gmail.com", role = c("aut", "ctb")) )
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Spatial Analysis for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>). It uses data from R package 'PakPC2017'.
Depends: R (>= 3.1)
Imports: dplyr, ggplot2, htmltools, htmlwidgets, leaflet, magrittr, PakPC2017, rgdal, scales, shiny, tidyr, tmap
Suggests: testthat
License: GPL-3
URL: https://github.com/MYaseen208/ppcSpatial
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-15 08:20:14 UTC; yaseen
Author: Muhammad Yaseen [aut, cre], Muhammad Arfan Dilber [aut, ctb]
Repository: CRAN
Date/Publication: 2018-02-16 16:52:31 UTC

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New package phenoCDM with initial version 0.0.2
Package: phenoCDM
Title: Continuous Development Models for Incremental Time-Series Analysis
Version: 0.0.2
Date: 2018-02-14
Authors@R: person("Bijan", "Seyednasrollah", email = "bijan.s.nasr@gmail.com", role = c("aut", "cre"))
Author: Bijan Seyednasrollah [aut, cre]
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Description: Using the Bayesian state-space approach, we developed a continuous development model to quantify dynamic incremental changes in the response variable. While the model was originally developed for daily changes in forest green-up, the model can be used to predict any similar process. The CDM can capture both timing and rate of nonlinear processes. Unlike statics methods, which aggregate variations into a single metric, our dynamic model tracks the changing impacts over time. The CDM accommodates nonlinear responses to variation in predictors, which changes throughout development.
Depends: rjags
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
BugReports: https://github.com/bnasr/phenoCDM/issues
NeedsCompilation: no
Packaged: 2018-02-14 22:35:19 UTC; bijan
Repository: CRAN
Date/Publication: 2018-02-16 16:48:17 UTC

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New package genBart with initial version 1.0.0
Package: genBart
Type: Package
Title: Generate 'BART' File
Version: 1.0.0
Authors@R: c( person("Jacob", "Cardenas", email = "jacob.cardenas@bswhealth.org", role = c("aut", "cre")), person("Jacob", "Turner", role = "aut"), person("Derek", "Blankenship", role = "aut") )
Description: A set of functions to generate and format results from statistical analyses of a wide range of high throughput experiments that can then be uploaded into the 'BART' (Bio-Statistical Analysis Reporting Tool) 'shiny' app <https://github.com/jcardenas14/BART>. The app provides users with tools to visualize and efficiently sift through large amounts of data and results.
Depends: R (>= 3.4.0)
Imports: clValid (>= 0.6-6), data.table (>= 1.10.4), fastcluster (>= 1.1.22), ggplot2 (>= 2.2.1), grid (>= 3.3.3), gtools (>= 3.5.0), limma (>= 3.30.13), NMF (>= 0.20.6), pca3d (>= 0.10), psych (>= 1.7.3.21), qusage (>= 2.6.1), RColorBrewer (>= 1.1-2), reshape2 (>= 1.4.2), rmarkdown (>= 1.5), scales (>= 0.4.1), shiny (>= 1.0.3), shinydashboard (>= 0.5.3), shinyjs (>= 0.9), statmod (>= 1.2.2), stats (>= 3.3.3), stringr (>= 1.2.0), tools (>= 3.3.3), VennDiagram (>= 1.6.17)
Suggests: DESeq2 (>= 1.14.1), edgeR (>= 3.16.5), knitr (>= 1.15.1), SummarizedExperiment (>= 1.1.6), testthat
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
RoxygenNote: 6.0.1
biocViews: Microarray, RNASeq, AnnotationData
NeedsCompilation: no
Packaged: 2018-02-14 20:56:10 UTC; e89628
Author: Jacob Cardenas [aut, cre], Jacob Turner [aut], Derek Blankenship [aut]
Maintainer: Jacob Cardenas <jacob.cardenas@bswhealth.org>
Repository: CRAN
Date/Publication: 2018-02-16 16:36:31 UTC

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Package PakPC2017 updated to version 1.0.0 with previous version 0.4.0 dated 2017-12-25

Title: Pakistan Population Census 2017
Description: Provides data sets and functions for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>).
Author: Muhammad Yaseen [aut, cre], Muhammad Arfan Dilber [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>

Diff between PakPC2017 versions 0.4.0 dated 2017-12-25 and 1.0.0 dated 2018-02-16

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Package dataPreparation updated to version 0.3.5 with previous version 0.3.4 dated 2017-12-20

Title: Automated Data Preparation
Description: Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of data.table efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Author: Emmanuel-Lin Toulemonde [aut, cre]
Maintainer: Emmanuel-Lin Toulemonde <el.toulemonde@protonmail.com>

Diff between dataPreparation versions 0.3.4 dated 2017-12-20 and 0.3.5 dated 2018-02-16

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Package BayesNetBP updated to version 1.3.0 with previous version 1.2.1 dated 2017-06-06

Title: Bayesian Network Belief Propagation
Description: Belief propagation methods in Bayesian Networks to propagate evidence through the network. The implementation of these methods are based on the article: Cowell, RG (2005). Local Propagation in Conditional Gaussian Bayesian Networks <http://www.jmlr.org/papers/volume6/cowell05a/>.
Author: Han Yu
Maintainer: Han Yu <hyu9@buffalo.edu>

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Package NLMR updated to version 0.2.1 with previous version 0.2 dated 2018-01-09

Title: Simulating Neutral Landscape Models
Description: Provides neutral landscape models (Gardner et al. 1987 <doi:10.1007/BF02275262>, With 1997 <doi:10.1046/j.1523-1739.1997.96210.x>) that can easily extend in existing landscape analyses. Neutral landscape models range from "hard" neutral models (completely random distributed), to "soft" neutral models (definable spatial characteristics) and generate landscape patterns that are independent of ecological processes. Thus, these patterns can be used as null models in landscape ecology. 'NLMR' combines a large number of algorithms from other published software for simulating neutral landscapes (Saura & Martínez 2000 <doi:10.1023/A:1008107902848>, Etherington et al. 2015 <doi:10.1111/2041-210X.12308>) and includes utility functions to classify and combine the multiple landscapes. The simulation results are obtained in a geospatial data format (raster* objects from the 'raster' package) and can, therefore, be used in any sort of raster data operation that is performed with standard observation data.
Author: Marco Sciaini [aut, cre], Matthias Fritsch [aut], Craig Simpkins [aut], Cédric Scherer [ctb] (Implemented nlm_neigh)
Maintainer: Marco Sciaini <sciaini.marco@gmail.com>

Diff between NLMR versions 0.2 dated 2018-01-09 and 0.2.1 dated 2018-02-16

 NLMR-0.2.1/NLMR/DESCRIPTION                                                                            |   22 +-
 NLMR-0.2.1/NLMR/MD5                                                                                    |   81 +++++-----
 NLMR-0.2.1/NLMR/NAMESPACE                                                                              |    1 
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 NLMR-0.2.1/NLMR/vignettes/bestiary.Rmd                                                                 |    4 
 NLMR-0.2.1/NLMR/vignettes/faq.Rmd                                                                      |    2 
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Package PPCI updated to version 0.1.1 with previous version 0.1.0 dated 2017-11-22

Title: Projection Pursuit for Cluster Identification
Description: Implements recently developed projection pursuit algorithms for finding optimal linear cluster separators. The clustering algorithms use optimal hyperplane separators based on minimum density, Pavlidis et. al (2016) <https://jmlr.csail.mit.edu/papers/volume17/15-307/15-307.pdf>; minimum normalised cut, Hofmeyr (2017) <doi:10.1109/TPAMI.2016.2609929>; and maximum variance ratio clusterability, Hofmeyr and Pavlidis (2015) <doi:10.1109/SSCI.2015.116>.
Author: David Hofmeyr <dhofmeyr@sun.ac.za> [aut, cre] Nicos Pavlidis <n.pavlidis@lancaster.ac.uk> [aut]
Maintainer: David Hofmeyr <dhofmeyr@sun.ac.za>

Diff between PPCI versions 0.1.0 dated 2017-11-22 and 0.1.1 dated 2018-02-16

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Package worldmet updated to version 0.8.3 with previous version 0.8.0 dated 2017-12-18

Title: Import Surface Meteorological Data from NOAA Integrated Surface Database (ISD)
Description: Functions to import data from more than 30,000 surface meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

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Package GetDFPData updated to version 0.6 with previous version 0.5 dated 2017-12-07

Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.bmfbovespa.com.br/en_us/products/listed-equities-and-derivatives/equities/listed-companies.htm>. These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetDFPData versions 0.5 dated 2017-12-07 and 0.6 dated 2018-02-16

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Package nlme updated to version 3.1-135.5 with previous version 3.1-135 dated 2017-12-31

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>

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Package meta4diag updated to version 2.0.7 with previous version 2.0.6 dated 2017-11-01

Title: Meta-Analysis for Diagnostic Test Studies
Description: Bayesian inference analysis for bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximation with INLA. A purpose built graphic user interface is available. The installation of R package INLA is compulsory for successful usage. The INLA package can be obtained from <http://www.r-inla.org>. We recommend the testing version, which can be downloaded by running: install.packages("INLA", repos="http://www.math.ntnu.no/inla/R/testing").
Author: Jingyi Guo <jingyi.guo@math.ntnu.no> and Andrea Riebler <andrea.riebler@math.ntnu.no>
Maintainer: Jingyi Guo <jingyi.guo@math.ntnu.no>

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Package mdmb updated to version 0.6-17 with previous version 0.5-27 dated 2018-01-22

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. The regression model can be nonlinear (e.g., including interaction or quadratic effects). Multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package googleAnalyticsR updated to version 0.5.0 with previous version 0.4.2 dated 2017-10-20

Title: Google Analytics API into R
Description: Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, and Multi-Channel Funnel API.
Author: Mark Edmondson [aut, cre], Artem Klevtsov [ctb], Johann deBoer [ctb], David Watkins [ctb], Olivia Brode-Roger [ctb], Jas Sohi [ctb], Zoran Selinger [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

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Package ggmuller updated to version 0.5.1 with previous version 0.4 dated 2018-02-08

Title: Create Muller Plots of Evolutionary Dynamics
Description: Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits).
Author: Robert Noble [aut, cre] (<https://orcid.org/0000-0002-8057-4252>)
Maintainer: Robert Noble <robjohnnoble@gmail.com>

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Package getopt updated to version 1.20.2 with previous version 1.20.1 dated 2017-11-29

Title: C-Like 'getopt' Behavior
Description: Package designed to be used with Rscript to write ``#!'' shebang scripts that accept short and long flags/options. Many users will prefer using instead the packages optparse or argparse which add extra features like automatically generated help option and usage, support for default values, positional argument support, etc.
Author: Allen Day. Contributions from Trevor L Davis and Roman Zenka.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>

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