Sat, 30 Jul 2016

New package WPC with initial version 1.0
Package: WPC
Type: Package
Title: Weighted Predictiveness Curve
Version: 1.0
Date: 2016-07-29
Author: Hui Yang <huiy@amgen.com>, Rui Tang <rui_rui_tang@vrtx.com>, Jing Huang <jinghuang0@gmail.com>
Maintainer: Hui Yang <huiy@amgen.com>
Description: Implementing weighted predictiveness curve to visualize the marker-by-treatment relationship and measure the performance of biomarkers for guiding treatment decision.
License: LGPL (>= 2)
Depends: survival, msm
LazyData: true
NeedsCompilation: no
Packaged: 2016-07-29 22:40:04 UTC; huiy
Repository: CRAN
Date/Publication: 2016-07-30 09:30:28

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New package time2event with initial version 0.1.0
Package: time2event
Type: Package
Title: Survival and Competing Risk Analyses with Time-to-Event Data as Covariates
Version: 0.1.0
Author: Seongho Kim
Maintainer: Seongho Kim <biostatistician.kim@gmail.com>
Depends: survival, timereg
Description: Cox proportional hazard and competing risk regression analyses can be performed with time-to-event data as covariates.
License: GPL-2
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-07-29 22:55:49 UTC; kimse
Repository: CRAN
Date/Publication: 2016-07-30 09:30:37

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Package sjstats updated to version 0.3.0 with previous version 0.2.0 dated 2016-06-20

Title: Collection of Convenient Functions for Common Statistical Computations
Description: Collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort (like standard errors or root mean squared errors). Second, these shortcut functions are generic (if appropriate), and can be applied not only to vectors, but also to other objects as well (e.g., the Coefficient of Variation can be computed for vectors, linear models, or linear mixed models; the r2()-function returns the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects). The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models and mixed effects models. However, some of the functions also deal with other statistical measures, like Cronbach's Alpha, Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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New package spdplyr with initial version 0.1.2
Package: spdplyr
Type: Package
Version: 0.1.2
Title: Data Manipulation Verbs for the Spatial Classes
Description: Methods for 'dplyr' verbs for 'sp' 'Spatial' classes. The basic verbs that modify data attributes, remove or re-arrange rows are supported and provide complete 'Spatial' analogues of the input data. The group by and summarize workflow returns a non-topological spatial union. There is limited support for joins, with left and inner to copy attributes from another table.
Authors@R: c(person("Michael D.","Sumner", role = c("aut", "cre"), email = "mdsumner@gmail.com"), person("Joscha", "Legewie", role = "ctb"))
URL: https://github.com/mdsumner/spdplyr
BugReports: https://github.com/mdsumner/spdplyr/issues
Depends: R (>= 3.2.3), dplyr, sp
Imports: lazyeval, methods, spbabel, tibble
Suggests: testthat, maptools, raster, rmarkdown, knitr, covr
VignetteBuilder: knitr
LazyData: yes
License: GPL-3
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-29 22:50:59 UTC; michae_sum
Author: Michael D. Sumner [aut, cre], Joscha Legewie [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-30 09:30:36

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Package RSelenium updated to version 1.4.0 with previous version 1.3.5 dated 2014-10-26

Title: R Bindings for Selenium WebDriver
Description: The RSelenium package provides a set of R bindings for the Selenium 2.0 WebDriver using the JsonWireProtocol. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.
Author: John Harrison <johndharrison0@gmail.com>
Maintainer: John Harrison <johndharrison0@gmail.com>

Diff between RSelenium versions 1.3.5 dated 2014-10-26 and 1.4.0 dated 2016-07-30

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Package QCA3 updated to version 0.0-8 with previous version 0.0-7 dated 2014-04-27

Title: Yet Another Package for Qualitative Comparative Analysis
Description: A set of functions for Qualitative Comparative Analysis (QCA). It can be used for various types of QCA (csQCA, mvQCA fsQCA and crisp set TQCA and time-serious QCA). It has methods for simplifying assumption, contradictory simplifying assumption.
Author: Ronggui HUANG
Maintainer: Ronggui HUANG<ronggui.huang@gmail.com>

Diff between QCA3 versions 0.0-7 dated 2014-04-27 and 0.0-8 dated 2016-07-30

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Package oec updated to version 1.0.3 with previous version 1.0.2 dated 2016-07-27

Title: The Observatory of Economic Complexity
Description: Use The Observatory of Economic Complexity's API from R console to obtain international trade data to create spreadsheets (csv format) and D3Plus visualizations.
Author: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>
Maintainer: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>

Diff between oec versions 1.0.2 dated 2016-07-27 and 1.0.3 dated 2016-07-30

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Package NNS updated to version 0.1.9.4 with previous version 0.1.9.2 dated 2016-06-14

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>

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Package ggpmisc updated to version 0.2.10 with previous version 0.2.9 dated 2016-06-18

Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Provides new statistics to locate and tag peaks and valleys in 2D plots, a statistics to add a label with the equation of a polynomial fitted with lm(), or R^2 or adjusted R^2 or information criteria for any model fitted with function lm(). Additional statistics give access to functions in package 'broom'. Provides a function for flexibly converting time series to data frames suitable for plotting with ggplot(). In addition provides two statistics and two geometries useful for diagnosing what data are passed to compute_group() and compute_panel() functions and to geometries.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Fri, 29 Jul 2016

Package visreg updated to version 2.3-0 with previous version 2.2-2 dated 2016-02-06

Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'randomForest', etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

Diff between visreg versions 2.2-2 dated 2016-02-06 and 2.3-0 dated 2016-07-29

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Package toaster updated to version 0.5.2 with previous version 0.5.1 dated 2016-03-23

Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster') embraces simple 2-step approach: compute in Aster - visualize and analyze in R. Its `compute` functions use combination of parallel SQL, SQL-MR and SQL-GR executing in Aster database - highly scalable parallel and distributed analytical platform. Then `create` functions visualize results with boxplots, scatterplots, histograms, heatmaps, word clouds, maps, networks, or slope graphs. Advanced options such as faceting, coloring, labeling, and others are supported with most visualizations.
Author: Gregory Kanevsky [aut, cre]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>

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Package IntNMF updated to version 1.1 with previous version 1.0 dated 2016-04-23

Title: Integrative Clustering of Multiple Genomic Dataset
Description: Carries out integrative clustering analysis using multiple types of genomic dataset.
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Prabhakar Chalise <pchalise@kumc.edu>

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Package InterSIM updated to version 2.1 with previous version 2.0 dated 2015-12-14

Title: Simulation of Inter-Related Genomic Datasets
Description: Generates three inter-related genomic datasets : methylation, gene expression and protein expression.
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Prabhakar Chalise <pchalise@kumc.edu>

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Package extraDistr updated to version 1.8.1 with previous version 1.8.0 dated 2016-07-28

Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>

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Package EpiModel updated to version 1.2.7 with previous version 1.2.6 dated 2016-05-24

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic agent-based models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an easy API for extending these templates to address novel scientific research aims.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Emily Beylerian [ctb], Skye Bender-deMoll [ctb], Kevis Weiss [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>

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Package crawl updated to version 2.0.1 with previous version 2.0 dated 2016-02-26

Title: Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data
Description: The Correlated Random Walk Library of R functions was designed for fitting continuous-time correlated random walk models with time indexed covariates. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>

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Package rstanarm updated to version 2.11.1 with previous version 2.10.1 dated 2016-06-25

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates pre-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], Trustees of Columbia University [cph], R Core Deveopment Team [cph] (R/pp_data.R, 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 presens updated to version 2.1.0 with previous version 2.0.0 dated 2016-03-14

Title: Interface for PreSens Fiber Optic Data
Description: Makes output files from select PreSens Fiber Optic Oxygen Transmitters easier to work with in R. See <http://www.presens.de> for more information about PreSens (Precision Sensing GmbH). Note: this package is neither created nor maintained by PreSens.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>

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Package onewaytests updated to version 1.2 with previous version 1.1 dated 2015-12-03

Title: One-Way Independent Groups Design
Description: Two or more samples in one-way independent groups design are compared via different tests.
Author: Osman Dag, Anil Dolgun, N. Meric Konar
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

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Package mosaic updated to version 0.14.4 with previous version 0.14 dated 2016-06-16

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 <rpruim@calvin.edu>, Daniel T. Kaplan <kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Package emIRT updated to version 0.0.7 with previous version 0.0.6 dated 2016-03-22

Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory (IRT) models. The current implementation includes IRT models for binary and ordinal responses, along with dynamic and hierarchical IRT models with binary responses. The latter two models are derived and implemented using variational EM. Subsequent edits also include variational network and text scaling models.
Author: Kosuke Imai <kimai@princeton.edu>, James Lo <lojames@usc.edu>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: James Lo <lojames@usc.edu>

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Package DVHmetrics updated to version 0.3.6 with previous version 0.3.5 dated 2016-03-09

Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics as well as generalized equivalent uniform dose (gEUD), biologically effective dose (BED), equivalent dose in 2 Gy fractions (EQD2), normal tissue complication probability (NTCP), and tumor control probability (TCP). Show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre], Heiko Karle [aut], Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>

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Package deconstructSigs updated to version 1.8.0 with previous version 1.6.0 dated 2016-01-29

Title: Identifies Signatures Present in a Tumor Sample
Description: Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.
Author: Rachel Rosenthal
Maintainer: Rachel Rosenthal <rachel.rosenthal.14@ucl.ac.uk>

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Package blscrapeR updated to version 0.4.2 with previous version 0.4.1 dated 2016-07-24

Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from the Bureau of Labor Statistics, which is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>

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Package BayesPiecewiseICAR updated to version 0.1.1 with previous version 0.1.0 dated 2016-07-27

Title: Hierarchical Bayesian Model for a Hazard Function
Description: Fits a piecewise exponential hazard to survival data using a Hierarchical Bayesian model with an Intrinsic Conditional Autoregressive formulation for the spatial dependency in the hazard rates for each piece. This function uses Metropolis- Hastings-Green MCMC to allow the number of split points to vary. This function outputs graphics that display the histogram of the number of split points and the trace plots of the hierarchical parameters. The function outputs a list that contains the posterior samples for the number of split points, the location of the split points, and the log hazard rates corresponding to these splits. Additionally, this outputs the posterior samples of the two hierarchical parameters, Mu and Sigma^2.
Author: person("Andrew", "Chapple", email = "Andrew.G.Chapple@rice.edu", role = c("aut", "cre"))
Maintainer: Andrew Chapple <Andrew.G.Chapple@rice.edu>

Diff between BayesPiecewiseICAR versions 0.1.0 dated 2016-07-27 and 0.1.1 dated 2016-07-29

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Package oc updated to version 0.96 with previous version 0.95 dated 2014-09-26

Title: OC Roll Call Analysis Software
Description: Estimates Optimal Classification scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
Author: Keith Poole <ktpoole@uga.edu>, Jeffrey Lewis <jblewis@ucla.edu>, James Lo <lojames@usc.edu> and Royce Carroll <rcarroll@rice.edu>
Maintainer: James Lo <lojames@usc.edu>

Diff between oc versions 0.95 dated 2014-09-26 and 0.96 dated 2016-07-29

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Package MCI updated to version 1.2.0 with previous version 1.1.1 dated 2016-06-29

Title: Multiplicative Competitive Interaction (MCI) Model
Description: The Multiplicative Competitive Interaction (MCI) Model by Nakanishi & Cooper (1974) <DOI:10.2307/3151146> is an econometric model for analyzing market shares and/or market areas and is closely related to the Huff model. The functions in this package include fitting the MCI model, MCI shares simulations, the log-centering transformation of MCI datasets, creation of interaction matrices and tools for data preparation. Additionally, the package provides applications for the Huff model, including a non-linear fitting algorithm.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>

Diff between MCI versions 1.1.1 dated 2016-06-29 and 1.2.0 dated 2016-07-29

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Package eggCounts updated to version 1.1-1 with previous version 1.1 dated 2016-07-06

Title: Hierarchical Modelling of Faecal Egg Counts
Description: An implementation of hierarchical models for faecal egg count data to assess anthelmintic efficacy. Bayesian inference is done via MCMC sampling using Stan.
Author: Craig Wang [cre, aut], Michaela Paul [aut], Reinhard Furrer [ctb], Trustees of Columbia University [cph] (rstanarm)
Maintainer: Craig Wang <craig.wang@uzh.ch>

Diff between eggCounts versions 1.1 dated 2016-07-06 and 1.1-1 dated 2016-07-29

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Package basicspace updated to version 0.18 with previous version 0.17 dated 2016-03-09

Title: Recovering a Basic Space from Issue Scales
Description: Conducts Aldrich-McKelvey and Blackbox Scaling to Recover Latent Dimensions of Judgment.
Author: Keith Poole <ktpoole@uga.edu>, Howard Rosenthal <hr31@nyu.edu>, Jeffrey Lewis <jblewis@ucla.edu>, James Lo <lojames@usc.edu> and Royce Carroll <rcarroll@rice.edu>
Maintainer: James Lo <lojames@usc.edu>

Diff between basicspace versions 0.17 dated 2016-03-09 and 0.18 dated 2016-07-29

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New package bife with initial version 0.1
Package: bife
Type: Package
Title: Binary Choice Models with Fixed Effects
Version: 0.1
Date: 2016-07-28
Authors@R: c(person("Amrei", "Stammann", email = "amrei.stammann@hhu.de", role = c("aut", "cre")), person("Daniel", "Czarnowske", email = "d.czarnowske@gmx.de", role = "aut"), person("Florian", "Heiss", email = "florian.heiss@hhu.de", role = "aut"), person("Daniel", "McFadden", email = "mcfadden@econ.berkeley.edu", role = "ctb"))
Description: Estimates fixed effects binary choice models (logit and probit) with potentially many individual fixed effects and computes average partial effects. Incidental parameter bias can be reduced with a bias-correction proposed by Hahn and Newey (2004) <doi:10.1111/j.1468-0262.2004.00533.x>.
License: GPL (>= 2)
Depends: R (>= 2.10)
Imports: Rcpp (>= 0.12.5), Formula, stats
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11
RoxygenNote: 5.0.1
LazyData: true
Suggests: knitr, rmarkdown, survival, ggplot2
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-07-29 10:38:23 UTC; Daniel
Author: Amrei Stammann [aut, cre], Daniel Czarnowske [aut], Florian Heiss [aut], Daniel McFadden [ctb]
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Repository: CRAN
Date/Publication: 2016-07-29 13:36:25

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New package SPreFuGED with initial version 1.0
Package: SPreFuGED
Type: Package
Title: Selecting a Predictive Function for a Given Gene Expression Data
Version: 1.0
Date: 2016-07-27
Author: Victor L Jong, Kit CB Roes & Marinus JC Eijkemans
Maintainer: Victor L Jong <v.l.jong@umcutrecht.nl>
Description: The recent advancement of high-throughput technologies has led to frequent utilization of gene expression and other "omics" data for toxicological, diagnostic or prognostic studies in and clinical applications. Unlike in classical predictions where the number of samples is greater than the number of variables (n>p), the challenge faced with prediction using "omics" data is that the number of parameters greatly exceeds the number of samples (p>>n). To solve this curse of dimensionality problem, several predictive functions have been proposed for direct and probabilistic classification and survival predictions. Nevertheless, these predictive functions have been shown to perform differently across datasets. Comparing predictive functions and choosing the best is computationally intensive and leads to selection bias. Thus, the question which function should one choose for a given dataset is to be ascertained. This package implements the approach proposed by Jong et al., (2016) to address this question.
Depends: R(>= 3.2.4)
Imports: stats, methods, utils, Biobase, CMA, lme4, lattice, limma, boot, mvtnorm
Suggests: e1071, MASS, class, nnet, glmnet, randomForest
License: GPL (>= 2)
LazyData: True
NeedsCompilation: no
Packaged: 2016-07-29 08:20:11 UTC; jonglih
Repository: CRAN
Date/Publication: 2016-07-29 12:35:58

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New package microcontax with initial version 1.0
Package: microcontax
Type: Package
Title: The ConTax Data Package
Version: 1.0
Date: 2016-07-28
Author: Hilde Vinje, Kristian Hovde Liland, Lars Snipen.
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Description: The consensus taxonomy for prokaryotes is a set of data-sets for best possible taxonomic classification based on 16S rRNA sequence data.
License: GPL-2
Depends: R (>= 3.0.0)
Imports: microseq
Suggests: microcontax.data
Additional_repositories: http://repository.umb.no/R
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-29 09:08:39 UTC; larssn
Repository: CRAN
Date/Publication: 2016-07-29 12:35:57

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New package SpATS with initial version 1.0-4
Package: SpATS
Type: Package
Title: Spatial Analysis of Field Trials with Splines
Version: 1.0-4
Date: 2016-06-24
Authors@R: c( person("Maria Xose Rodriguez-Alvarez", email = "mxrodriguez@uvigo.es", role = c("aut", "cre")), person("Martin Boer", role = "aut"), person("Paul Eilers", role = "aut"), person("Fred van Eeuwijk", role = "ctb"))
Imports: stats, grDevices, graphics, fields, plot3Drgl, spam, data.table
Description: Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.
License: GPL
NeedsCompilation: no
Packaged: 2016-07-29 07:54:07 UTC; Cote
Author: Maria Xose Rodriguez-Alvarez [aut, cre], Martin Boer [aut], Paul Eilers [aut], Fred van Eeuwijk [ctb]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@uvigo.es>
Repository: CRAN
Date/Publication: 2016-07-29 10:36:41

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Package RCPmod updated to version 2.142 with previous version 2.141 dated 2016-07-29

Title: Regions of Common Profiles Modelling with Mixtures-of-Experts
Description: Identifies regions of common (species) profiles (RCPs), possibly when sampling artefacts are present. Within a region the probability of sampling all species remains approximately constant. This is performed using mixtures-of-experts models. The package also contains associated methods, such as diagnostics.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>

Diff between RCPmod versions 2.141 dated 2016-07-29 and 2.142 dated 2016-07-29

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New package peakRAM with initial version 1.0.0
Package: peakRAM
Title: Monitor the Total and Peak RAM Used by an Expression or Function
Version: 1.0.0
URL: http://github.com/tpq/peakRAM
BugReports: http://github.com/tpq/peakRAM/issues
Authors@R: c( person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")) )
Description: When working with big datasets, RAM conservation is critically important. However, it is not always enough to just monitor the size of the objects created. So-called "copy-on-modify" behavior, characteristic of R, means that some expressions or functions may require an unexpectedly large amount of RAM overhead. For example, replacing a single value in a matrix duplicates that matrix in the backend, making this task require twice as much RAM as that used by the matrix itself. This package makes it easy to monitor the total and peak RAM used so that developers can quickly identify and eliminate RAM hungry code.
License: GPL-2
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Depends: R (>= 3.2.2)
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2016-07-29 05:04:32 UTC; thom
Author: Thomas Quinn [aut, cre]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-29 07:38:22

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Package KFAS updated to version 1.2.4 with previous version 1.2.3 dated 2016-06-22

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: Functions for Kalman filtering, smoothing, forecasting and simulation of multivariate exponential family state space models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>

Diff between KFAS versions 1.2.3 dated 2016-06-22 and 1.2.4 dated 2016-07-29

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Package sbrl updated to version 1.2 with previous version 1.1 dated 2016-07-24

Title: Scalable Bayesian Rule Lists Model
Description: An implementation of Scalable Bayesian Rule Lists Algorithm.
Author: Hongyu Yang [aut, cre], Morris Chen [ctb], Cynthia Rudin [aut, ctb], Margo Seltzer [aut, ctb]
Maintainer: Hongyu Yang <hongyuy@mit.edu>

Diff between sbrl versions 1.1 dated 2016-07-24 and 1.2 dated 2016-07-29

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Package rsvd updated to version 0.6 with previous version 0.3 dated 2015-11-13

Title: Randomized Singular Value Decomposition
Description: Randomized singular value decomposition (rsvd) is a very fast probabilistic algorithm that can be used to compute the near optimal low-rank singular value decomposition of massive data sets with high accuracy. SVD plays a central role in data analysis and scientific computing. SVD is also widely used for computing (randomized) principal component analysis (PCA), a linear dimensionality reduction technique. Randomized PCA (rpca) uses the approximated singular value decomposition to compute the most significant principal components. This package also includes a function to compute (randomized) robust principal component analysis (RPCA). In addition several plot functions are provided.
Author: N. Benjamin Erichson [aut, cre]
Maintainer: N. Benjamin Erichson <nbe@st-andrews.ac.uk>

Diff between rsvd versions 0.3 dated 2015-11-13 and 0.6 dated 2016-07-29

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Package rstan updated to version 2.11.1 with previous version 2.10.1 dated 2016-06-24

Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut], Jonah Gabry [aut], Ben Goodrich [cre, aut], Daniel Lee [ctb], Krzysztof Sakrejda [ctb], Trustees of Columbia University [cph], Oleg Sklyar [cph] (R/cxxfunplus.R), The R Core Team [cph] (R/pairs.R), Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R), Hadley Wickham [cph] (R/rtools.R), Joel de Guzman [cph] (Boost), John Fletcher [cph] (Boost), Thomas Heller [cph] (Boost), Eric Niebler [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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Package RCPmod updated to version 2.141 with previous version 1.4 dated 2013-11-02

Title: Regions of Common Profiles Modelling with Mixtures-of-Experts
Description: Identifies regions of common (species) profiles (RCPs), possibly when sampling artefacts are present. Within a region the probability of sampling all species remains approximately constant. This is performed using mixtures-of-experts models. The package also contains associated methods, such as diagnostics.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@csiro.au>

Diff between RCPmod versions 1.4 dated 2013-11-02 and 2.141 dated 2016-07-29

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Package prodigenr updated to version 0.3.0 with previous version 0.2.7 dated 2016-05-14

Title: Research Project Directory Generator
Description: Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).
Author: Luke Johnston [aut, cre]
Maintainer: Luke Johnston <lwjohnst@gmail.com>

Diff between prodigenr versions 0.2.7 dated 2016-05-14 and 0.3.0 dated 2016-07-29

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Package jqr updated to version 0.2.4 with previous version 0.2.3 dated 2016-05-10

Title: Client for 'jq', a JSON Processor
Description: Client for 'jq', a JSON processor (<http://stedolan.github.io/jq/>), written in C. 'jq' allows the following with JSON data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.
Author: Rich FitzJohn [aut], Jeroen Ooms [aut], Scott Chamberlain [aut, cre], Stefan Milton Bache [aut], Stephen Dolan [aut, cph] (jq library), jq contributors [ctb] (jq library; authors listed in inst/AUTHORS.jq), Free Software Foundation [ctb, cph] (parser code in src/parser.c), David M Gay [ctb, cph] (code in src/jv_dtoa.c)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between jqr versions 0.2.3 dated 2016-05-10 and 0.2.4 dated 2016-07-29

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New package NetRep with initial version 1.0.2
Package: NetRep
Type: Package
Title: Permutation Testing Network Module Preservation Across Datasets
Version: 1.0.2
Date: 2016-07-28
Authors@R: person(given="Scott", family="Ritchie", email="sritchie73@gmail.com", role=c("aut", "cre"))
BugReports: https://github.com/InouyeLab/NetRep/issues
Description: Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing.
License: GPL-2
Depends: R (>= 3.0.2), methods
Imports: foreach, Rcpp (>= 0.11), statmod, RhpcBLASctl, abind, RColorBrewer, utils, stats, graphics, grDevices, ref
Suggests: bigmemory, testthat, knitr, rmarkdown
LinkingTo: Rcpp, BH, RcppArmadillo (>= 0.4)
SystemRequirements: A compiler with C++11 support for the thread library, Requires Rtools >= 33 (i.e. R >= 3.3.0) to build on Windows.
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-07-29 00:08:29 UTC; scottr
Author: Scott Ritchie [aut, cre]
Maintainer: Scott Ritchie <sritchie73@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-29 06:40:57

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Package FinCal updated to version 0.6.3 with previous version 0.6.2 dated 2015-12-30

Title: Time Value of Money, Time Series Analysis and Computational Finance
Description: Package for time value of money calculation, time series analysis and computational finance.
Author: Felix Yanhui Fan <nolanfyh@gmail.com>
Maintainer: Felix Yanhui Fan <nolanfyh@gmail.com>

Diff between FinCal versions 0.6.2 dated 2015-12-30 and 0.6.3 dated 2016-07-29

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New package eAnalytics with initial version 0.1.0
Package: eAnalytics
Version: 0.1.0
Title: Dynamic Web Analytics for the Energy Industry
Description: A 'Shiny' web application for energy industry analytics. Take an overview of the industry, measure Key Performance Indicators, identify changes in the industry over time, and discover new relationships in the data.
URL: https://github.com/paulgovan/eanalytics
BugReports: https://github.com/paulgovan/eanalytics/issues
Authors@R: person("Paul", "Govan", email = "pgovan1@aggienetwork.com", role = c("aut", "cre"))
Depends: R (>= 2.10.0), plotly,
License: Apache License
LazyData: TRUE
Imports: d3heatmap, dplyr, DT, energyr, googleVis, leaflet, shiny, shinydashboard
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-29 03:50:00 UTC; paulgovan
Author: Paul Govan [aut, cre]
Maintainer: Paul Govan <pgovan1@aggienetwork.com>
Repository: CRAN
Date/Publication: 2016-07-29 07:05:04

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Package beanz updated to version 1.6 with previous version 1.5 dated 2016-07-06

Title: Bayesian Analysis of Heterogeneous Treatment Effect
Description: It is vital to assess the heterogeneity of treatment effects (HTE) when making health care decisions for an individual patient or a group of patients. Nevertheless, it remains challenging to evaluate HTE based on information collected from clinical studies that are often designed and conducted to evaluate the efficacy of a treatment for the overall population. The Bayesian framework offers a principled and flexible approach to estimate and compare treatment effects across subgroups of patients defined by their characteristics. This package allows users to explore a wide range of Bayesian HTE analysis models, and produce posterior inferences about HTE.
Author: Chenguang Wang [aut, cre], Ravi Varadhan [aut], Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>

Diff between beanz versions 1.5 dated 2016-07-06 and 1.6 dated 2016-07-29

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New package carpenter with initial version 0.2.0
Package: carpenter
Type: Package
Title: Build Common Tables of Summary Statistics for Reports
Version: 0.2.0
Authors@R: person("Luke", "Johnston", email = "lwjohnst@gmail.com", role = c("aut", "cre"))
Description: Mainly used to build tables that are commonly presented for bio-medical/health research, such as basic characteristic tables or descriptive statistics.
License: MIT + file LICENSE
LazyData: TRUE
Imports: dplyr, magrittr, tidyr, pander, utils, stats, lazyeval
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/lwjohnst86/carpenter
BugReports: https://github.com/lwjohnst86/carpenter/issues
NeedsCompilation: no
Packaged: 2016-07-29 01:20:40 UTC; luke
Author: Luke Johnston [aut, cre]
Maintainer: Luke Johnston <lwjohnst@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-29 06:41:05

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New package AhoCorasickTrie with initial version 0.1.0
Package: AhoCorasickTrie
Type: Package
Title: Fast Searching for Multiple Keywords in Multiple Texts
Version: 0.1.0
Authors@R: c(person("Matt", "Chambers", email="matt.chambers42@gmail.com", role=c("aut", "cre")), person("Tomas", "Petricek", role=c("aut", "cph")), person("Vanderbilt University", role="cph"))
Description: Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.
License: Apache License 2.0
URL: https://github.com/chambm/AhoCorasickTrie
BugReports: https://github.com/chambm/AhoCorasickTrie/issues
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.5)
LinkingTo: Rcpp
Suggests: Biostrings, microbenchmark
SystemRequirements: C++11
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-07-29 00:25:38 UTC; chambem2
Author: Matt Chambers [aut, cre], Tomas Petricek [aut, cph], Vanderbilt University [cph]
Maintainer: Matt Chambers <matt.chambers42@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-29 06:40:52

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Thu, 28 Jul 2016

Package sommer updated to version 2.0 with previous version 1.9 dated 2016-07-01

Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model equation solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>

Diff between sommer versions 1.9 dated 2016-07-01 and 2.0 dated 2016-07-28

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New package RcppGetconf with initial version 0.0.1
Package: RcppGetconf
Type: Package
Title: 'Rcpp' Interface for Querying System Configuration Variables
Version: 0.0.1
Date: 2016-07-26
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Description: The 'getconf' command-line tool provided by 'libc' allows querying of a large number of system variables. This package provides similar functionality.
Imports: Rcpp
LinkingTo: Rcpp
SystemRequirements: A POSIX system. Currently only Linux is known to work.
OS_type: unix
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-07-28 21:50:46.216302 UTC; edd
Repository: CRAN
Date/Publication: 2016-07-28 23:55:33

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Package Rankcluster updated to version 0.94 with previous version 0.93.1 dated 2016-01-12

Title: Model-Based Clustering for Multivariate Partial Ranking Data
Description: Implementation of a model-based clustering algorithm for ranking data. Multivariate rankings as well as partial rankings are taken into account. This algorithm is based on an extension of the Insertion Sorting Rank (ISR) model for ranking data, which is a meaningful and effective model parametrized by a position parameter (the modal ranking, quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity of the rank population is modelled by a mixture of ISR, whereas conditional independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez, Julien Jacques
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>

Diff between Rankcluster versions 0.93.1 dated 2016-01-12 and 0.94 dated 2016-07-28

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New package OptimalDesign with initial version 0.1
Package: OptimalDesign
Version: 0.1
Date: 2016-07-25
Title: Optimal Design
Author: Radoslav Harman, Lenka Filova
Maintainer: Lenka Filova <OptimalDesignR@gmail.com>
Description: Algorithms for D-, A- and IV-optimal designs of experiments. Some of the functions in this package require the 'gurobi' software and its accompanying R package. For their installation, please follow the instructions at <www.gurobi.com> and <http://www.gurobi.com/documentation>, respectively.
Enhances: gurobi, slam, Matrix
License: GPL-3
URL: < http://www.iam.fmph.uniba.sk/design/ >
NeedsCompilation: no
Packaged: 2016-07-27 19:53:11 UTC; Lenka
Repository: CRAN
Date/Publication: 2016-07-28 23:53:07

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New package noise with initial version 1.0
Package: noise
Type: Package
Title: Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data
Version: 1.0
Date: 2016-07-28
Author: Audrey Qiuyan Fu and Lior Pachter
Maintainer: Audrey Q. Fu <audreyqyfu@gmail.com>
Description: Functions to calculate estimates of intrinsic and extrinsic noise from the two-reporter single-cell experiment, as in Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186. Functions implement multiple estimators developed for unbiasedness or min Mean Squared Error (MSE) in Fu, A. Q. and Pachter, L. (2016). Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. <http://arxiv.org/abs/1601.03334>.
License: GPL (>= 2)
Depends: R (>= 2.10)
LazyLoad: yes
LazyData: yes
Imports: preprocessCore
NeedsCompilation: no
Packaged: 2016-07-28 22:34:14 UTC; audreyfu
Repository: CRAN
Date/Publication: 2016-07-29 00:45:54

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New package MultiBD with initial version 0.2.0
Package: MultiBD
Type: Package
Title: Multivariate Birth-Death Processes
Version: 0.2.0
Date: 2016-07-19
Author: Lam S.T. Ho [aut, cre], Marc A. Suchard [aut], Forrest W. Crawford [aut], Jason Xu [ctb], Vladimir N. Minin [ctb]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Description: Computationally efficient functions to provide direct likelihood-based inference for partially-observed multivariate birth-death processes. Such processes range from a simple Yule model to the complex susceptible-infectious-removed model in disease dynamics. Efficient likelihood evaluation facilitates maximum likelihood estimation and Bayesian inference.
License: Apache License 2.0
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.2), RcppParallel
LinkingTo: Rcpp, BH, RcppParallel
Suggests: testthat, knitr, rmarkdown, MCMCpack, ggplot2, matrixStats, plotrix
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-07-28 22:05:41 UTC; msuchard
Repository: CRAN
Date/Publication: 2016-07-29 00:29:18

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New package lexRankr with initial version 0.1.0
Package: lexRankr
Type: Package
Title: Extractive Summarization of Text with the LexRank Algorithm
Version: 0.1.0
Author: Adam Spannbauer <spannbaueradam@gmail.com>
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Description: An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: dplyr, tidyr, magrittr, stringr, SnowballC, igraph, proxy, tm
NeedsCompilation: no
Packaged: 2016-07-28 17:33:32 UTC; U775749
Repository: CRAN
Date/Publication: 2016-07-29 00:01:08

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Package generalhoslem updated to version 1.2.0 with previous version 1.0.1 dated 2016-07-10

Title: Goodness of Fit Tests for Logistic Regression Models
Description: Functions to assess the goodness of fit of binary, multinomial and ordinal logistic models. Included are the Hosmer-Lemshow tests (binary, multinomial and ordinal) and the Lipsitz and Pulkstenis-Robinson tests (ordinal).
Author: Matthew Jay [aut, cre]
Maintainer: Matthew Jay <matthew.jay.15@ucl.ac.uk>

Diff between generalhoslem versions 1.0.1 dated 2016-07-10 and 1.2.0 dated 2016-07-28

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Package intubate updated to version 0.99.2 with previous version 0.99.1 dated 2016-07-26

Title: Interface to Popular R Functions for Data Science Pipelines
Description: Interface to popular R functions with formulas, such as 'lm', so they can be included painlessly in data science pipelines implemented by 'magrittr' with the operator %>%.
Author: Roberto Bertolusso
Maintainer: Roberto Bertolusso <rbertolusso@rice.edu>

Diff between intubate versions 0.99.1 dated 2016-07-26 and 0.99.2 dated 2016-07-28

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New package files with initial version 0.0.1
Package: files
Title: Effective File Navigation from the R Console
Version: 0.0.1
Authors@R: person(c("Ronald", "E."), "Robertson",, "robertson.ron@husky.neu.edu", c("cre", "aut"))
Description: Functions for printing the contents of a folder as columns in a ragged-bottom data.frame and for viewing the details (size, time created, time modified, etc.) of a folder's top level contents.
Depends: R (>= 3.3.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 19:31:23 UTC; rer
Author: Ronald E. Robertson [cre, aut]
Maintainer: Ronald E. Robertson <robertson.ron@husky.neu.edu>
Repository: CRAN
Date/Publication: 2016-07-28 23:52:33

More information about files at CRAN
Permanent link

New package csvy with initial version 0.1.3
Package: csvy
Type: Package
Title: Import and Export CSV Data with a YAML Metadata Header
Version: 0.1.3
Date: 2016-07-28
Authors@R: person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com")
Description: Support for import from and export to the CSVY file format. CSVY is a file format that combines the simplicity of CSV (comma-separated values) with the metadata of other plain text and binary formats (JSON, XML, Stata, etc.) by placing a YAML header on top of a regular CSV.
Imports: utils, yaml
Suggests: data.table, readr, testthat, datasets
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-28 14:07:16 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-29 00:24:54

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New package CommEcol with initial version 1.6.4
Package: CommEcol
Type: Package
Title: Community Ecology Analyses
Version: 1.6.4
Depends: R (>= 2.10), vegan, ape, picante
Imports: gmp
Date: 2016-07-28
Author: Adriano Sanches Melo
Maintainer: Adriano Sanches Melo <asm.adrimelo@gmail.com>
Description: Autosimilarity curves, dissimilarity indexes that overweight rare species, phylogenetic and functional (pairwise and multisample) dissimilarity indexes and nestedness for phylogenetic, functional and other diversity metrics. This should be a complement to available packages, particularly 'vegan'.
License: GPL-2
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: commecol
Repository/R-Forge/Revision: 51
Repository/R-Forge/DateTimeStamp: 2016-07-28 21:06:33
Date/Publication: 2016-07-28 23:55:34
NeedsCompilation: no
Packaged: 2016-07-28 21:25:22 UTC; rforge

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New package BivUnifBin with initial version 1.0
Package: BivUnifBin
Type: Package
Title: Generation of Bivariate Uniform Data and Its Relation to Bivariate Binary Data
Version: 1.0
Date: 2016-07-27
Author: Hakan Demirtas, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Description: Simulation of bivariate uniform data with a full range of correlations based on two beta densities and computation of the tetrachoric correlation (correlation of bivariate uniform data) from the phi coefficient (correlation of bivariate binary data) and vice versa.
License: GPL-2 | GPL-3
Imports: BinOrdNonNor, rootSolve
NeedsCompilation: no
Repository: CRAN
Packaged: 2016-07-27 21:50:29 UTC; rawanallozi
Date/Publication: 2016-07-29 00:22:33

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Permanent link

New package anametrix with initial version 2.0.0
Package: anametrix
Type: Package
Title: Bidirectional Connector to Anametrix API
Version: 2.0.0
Date: 2016-07-20
Authors@R: c( person("Roman", "Jugai", role = "aut"), person("Caroline", "Cochet-Escartin", email = "caroline.escartin@ensighten.com", role = c("cre", "aut")), person("Gratien", "Desormeaux", role = "aut"))
Description: Offers a set of functions to upload/download data and metadata on Anametrix API <http://anametrix.com/>.
Depends: plyr, dplyr, RCurl, XML
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 16:05:17 UTC; carolineescartin
Author: Roman Jugai [aut], Caroline Cochet-Escartin [cre, aut], Gratien Desormeaux [aut]
Maintainer: Caroline Cochet-Escartin <caroline.escartin@ensighten.com>
Repository: CRAN
Date/Publication: 2016-07-27 18:06:33

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Permanent link

Package alakazam updated to version 0.2.4 with previous version 0.2.3 dated 2016-02-22

Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides immunoglobulin (Ig) sequence lineage reconstruction, diversity profiling, and amino acid property analysis. Also provides core functionality for other tools in the Change-O suite.
Author: Jason Vander Heiden [aut, cre], Namita Gupta [aut], Susanna Marquez [ctb], Daniel Gadala-Maria [ctb], Roy Jiang [ctb], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>

Diff between alakazam versions 0.2.3 dated 2016-02-22 and 0.2.4 dated 2016-07-28

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Package reproducer updated to version 0.1.6 with previous version 0.1.5 dated 2016-05-14

Title: Reproduce Statistical Analyses and Meta-Analyses
Description: The reproducer R package includes data analysis functions and data sets (e.g., related to software defect prediction) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb], Marian Jureczko [ctb] (Data contributor), Barbara Kitchenham [ctb] (Data and code contributor), David Budgen [ctb] (Data contributor), Pearl Brereton [ctb] (Data contributor), Jacky Keung [ctb] (Data contributor), Stuart Charters [ctb] (Data contributor), Shirley Gibbs [ctb] (Data contributor), Amnart Pohthong [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>

Diff between reproducer versions 0.1.5 dated 2016-05-14 and 0.1.6 dated 2016-07-28

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Package quanteda updated to version 0.9.8 with previous version 0.9.7-17 dated 2016-06-21

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre], Paul Nulty [aut], Kohei Watanabe [ctb], Benjamin Lauderdale [ctb], Adam Obeng [ctb], Pablo Barberá [ctb], Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

Diff between quanteda versions 0.9.7-17 dated 2016-06-21 and 0.9.8 dated 2016-07-28

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Package hnp updated to version 1.2-1 with previous version 1.2 dated 2016-03-08

Title: Half-Normal Plots with Simulation Envelopes
Description: Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
Author: Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral <rafael_moral@yahoo.com.br>

Diff between hnp versions 1.2 dated 2016-03-08 and 1.2-1 dated 2016-07-28

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More information about hnp at CRAN
Permanent link

Package extraDistr updated to version 1.8.0 with previous version 1.7.2 dated 2016-06-24

Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>

Diff between extraDistr versions 1.7.2 dated 2016-06-24 and 1.8.0 dated 2016-07-28

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 src/gpd-distribution.cpp                             |    3 
 src/gumbel-distribution.cpp                          |    3 
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 src/huber-distribution.cpp                           |    2 
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 src/lomax-distribution.cpp                           |    3 
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 src/power-distribution.cpp                           |    3 
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 src/shared.cpp                                       |   25 +++-
 src/shared.h                                         |    6 -
 src/slash-distribution.cpp                           |    4 
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Permanent link

Package StanHeaders updated to version 2.11.0 with previous version 2.10.0-2 dated 2016-06-24

Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between StanHeaders versions 2.10.0-2 dated 2016-06-24 and 2.11.0 dated 2016-07-28

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Package OpenMx updated to version 2.6.9 with previous version 2.6.8 dated 2016-07-16

Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications as things that can be generated and manipulated programmatically. Structural equation models may be specified with reticular action model matrices or paths, linear structural relations matrices or paths, or directly in matrix algebra. Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential equations, state space, and many others.
Author: Steven M. Boker [aut], Michael C. Neale [aut], Hermine H. Maes [aut], Michael J. Wilde [ctb], Michael Spiegel [aut], Timothy R. Brick [aut], Ryne Estabrook [aut], Timothy C. Bates [aut], Paras Mehta [ctb], Timo von Oertzen [ctb], Ross J. Gore [aut], Michael D. Hunter [aut], Daniel C. Hackett [ctb], Julian Karch [ctb], Andreas M. Brandmaier [ctb], Joshua N. Pritikin [aut, cre], Mahsa Zahery [aut], Robert M. Kirkpatrick [aut], Yang Wang [ctb], Charles Driver [ctb], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Association for Computing Machinery [cph], Dieter Kraft [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between OpenMx versions 2.6.8 dated 2016-07-16 and 2.6.9 dated 2016-07-28

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Package VariableScreening updated to version 0.1.1 with previous version 0.1.0 dated 2016-07-19

Title: High-Dimensional Screening for Semiparametric Longitudinal Regression
Description: Implements a screening procedure proposed by Wanghuan Chu, Runze Li and Matthew Reimherr (2016) <DOI:10.1214/16-AOAS912> for varying coefficient longitudinal models with ultra-high dimensional predictors . The effect of each predictor is allowed to vary over time, approximated by a low-dimensional B-spline. Within-subject correlation is handled using a generalized estimation equation approach with structure specified by the user. Variance is allowed to change over time, also approximated by a B-spline.
Author: Runze Li [aut], Wanghuan Chu [aut], Liying Huang [aut, cre], John Dziak [aut]
Maintainer: Liying Huang <lxh37@PSU.EDU>

Diff between VariableScreening versions 0.1.0 dated 2016-07-19 and 0.1.1 dated 2016-07-28

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Package sybilDynFBA updated to version 1.0.1 with previous version 1.0.0 dated 2016-06-02

Title: Dynamic FBA : Dynamic Flux Balance Analysis
Description: Implements dynamic FBA technique proposed by Varma et al 1994.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>

Diff between sybilDynFBA versions 1.0.0 dated 2016-06-02 and 1.0.1 dated 2016-07-28

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Package survminer updated to version 0.2.2 with previous version 0.2.1 dated 2016-04-23

Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table. Other functions are also available for visual examinations of 'cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre], Marcin Kosinski [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

Diff between survminer versions 0.2.1 dated 2016-04-23 and 0.2.2 dated 2016-07-28

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Package subselect updated to version 0.12-6 with previous version 0.12-5 dated 2015-04-13

Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima <jcadima@isa.utl.pt>

Diff between subselect versions 0.12-5 dated 2015-04-13 and 0.12-6 dated 2016-07-28

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Package orca updated to version 1.1-1 with previous version 1.1 dated 2015-03-10

Title: Computation of Graphlet Orbit Counts in Sparse Graphs
Description: Implements orbit counting using a fast combinatorial approach. Counts orbits of nodes and edges from edge matrix or data frame, or a graph object from the graph package.
Author: Tomaz Hocevar [aut], Janez Demsar [aut, cre]
Maintainer: Janez Demsar <janez.demsar@fri.uni-lj.si>

Diff between orca versions 1.1 dated 2015-03-10 and 1.1-1 dated 2016-07-28

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Package molaR updated to version 4.1 with previous version 4.0 dated 2016-05-20

Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph], Julia M. Winchester [aut, cph], Paul E. Morse [aut, cph], Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>

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More information about molaR at CRAN
Permanent link

Package imputeTestbench updated to version 2.0.2 with previous version 1.2.0 dated 2016-06-19

Title: Test Bench for Missing Data Imputing Models/Methods Comparison
Description: Provides a Test bench for comparison of missing data imputation models/methods. It compares imputing methods with reference to RMSE, MAE or MAPE parameters. It allows to add new proposed methods to test bench and to compare with other methods. The function 'append_method()' allows to add multiple numbers of methods to the existing methods available in test bench.
Author: Neeraj Bokde
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>

Diff between imputeTestbench versions 1.2.0 dated 2016-06-19 and 2.0.2 dated 2016-07-28

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Package gsl updated to version 2.1-1 with previous version 1.9-10.1 dated 2015-12-02

Title: Wrapper for the Gnu Scientific Library
Description: An R wrapper for some of the functionality of the Gnu Scientific Library.
Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and multimin by Andrew Clausen
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between gsl versions 1.9-10.1 dated 2015-12-02 and 2.1-1 dated 2016-07-28

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More information about gsl at CRAN
Permanent link

Package GLDreg updated to version 1.0.4 with previous version 1.0.3 dated 2015-07-04

Title: Fit GLD Regression Model and GLD Quantile Regression Model to Empirical Data
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su <allegro.su@gmail.com>

Diff between GLDreg versions 1.0.3 dated 2015-07-04 and 1.0.4 dated 2016-07-28

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Package CARBayesST updated to version 2.4 with previous version 2.3 dated 2016-06-15

Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, and full details are given in the vignette accompanying this package and the references in the help files. The creation of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

Diff between CARBayesST versions 2.3 dated 2016-06-15 and 2.4 dated 2016-07-28

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Package vines updated to version 1.1.5 with previous version 1.1.4 dated 2015-10-07

Title: Multivariate Dependence Modeling with Vines
Description: Implementation of the vine graphical model for building high-dimensional probability distributions as a factorization of bivariate copulas and marginal density functions. This package provides S4 classes for vines (C-vines and D-vines) and methods for inference, goodness-of-fit tests, density/distribution function evaluation, and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre], Marta Soto [aut], Joris Meys [ctb]
Maintainer: Yasser Gonzalez-Fernandez <ygonzalezfernandez@gmail.com>

Diff between vines versions 1.1.4 dated 2015-10-07 and 1.1.5 dated 2016-07-28

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Package jug updated to version 0.1.3 with previous version 0.1.2 dated 2016-05-10

Title: A Simple Web Framework for R
Description: A set of functions to ease the building of web APIs.
Author: Bart Smeets [aut, cre]
Maintainer: Bart Smeets <bartsmeets86@gmail.com>

Diff between jug versions 0.1.2 dated 2016-05-10 and 0.1.3 dated 2016-07-28

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Package formattable updated to version 0.2 with previous version 0.1.5 dated 2015-12-03

Title: Create 'Formattable' Data Structures
Description: Provides functions to create formattable vectors and data frames. 'Formattable' vectors are printed with text formatting, and formattable data frames are printed with multiple types of formatting in HTML to improve the readability of data presented in tabular form rendered in web pages.
Author: Kun Ren [aut, cre], Kenton Russell [aut]
Maintainer: Kun Ren <ken@renkun.me>

Diff between formattable versions 0.1.5 dated 2015-12-03 and 0.2 dated 2016-07-28

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Permanent link

Wed, 27 Jul 2016

Package SimSCRPiecewise updated to version 0.1.1 with previous version 0.1.0 dated 2016-07-27

Title: 'Simulates Univariate and Semi-Competing Risks Data Given Covariates and Piecewise Exponential Baseline Hazards'
Description: Contains two functions for simulating survival data from piecewise exponential hazards with a proportional hazards adjustment for covariates. The first function SimUNIVPiecewise simulates univariate survival data based on a piecewise exponential hazard, covariate matrix and true regression vector. The second function SimSCRPiecewise semi-competing risks data based on three piecewise exponential hazards, three true regression vectors and three matrices of patient covariates (which can be different or the same). This simulates from the Semi-Markov model of Lee et al (2015) given patient covariates, regression parameters, patient frailties and baseline hazard functions.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <Andrew.G.Chapple@rice.edu>

Diff between SimSCRPiecewise versions 0.1.0 dated 2016-07-27 and 0.1.1 dated 2016-07-27

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Package sEparaTe updated to version 0.2.1 with previous version 0.1.2 dated 2016-07-24

Title: Maximum Likelihood Estimation and Likelihood Ratio Test Functions for Separable Variance-Covariance Structures
Description: It combines maximum likelihood estimation of the parameters of matrix and 3rd-order tensor normal distributions with unstructured factor variance-covariance matrices, two procedures, and unbiased modified likelihood ratio testing of simple and double separability for variance-covariance structures, two procedures.
Author: Ameur Manceur [aut], Timothy Schwinghamer [aut, cre], Pierre Dutilleul [aut, cph]
Maintainer: Timothy Schwinghamer <schwinghamer@hotmail.com>

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Permanent link

Package plsVarSel updated to version 0.9 with previous version 0.8 dated 2016-06-15

Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least Squares. The methods include filter methods, wrapper methods and embedded methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

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Permanent link

New package placement with initial version 0.1.1
Package: placement
Type: Package
Title: Tools for Accessing the Google Maps API
Version: 0.1.1
Author: Derek Darves
Maintainer: Derek Darves <darves@gmail.com>
Description: The main functions in this package are drive_time (used for calculating distances between physical addresses or coordinates) and geocode_url (used for estimating the lat/long coordinates of a physical address). Optionally, it generates the cryptographic signatures necessary for making API calls with a Google for Work/Premium account within the geocoding process. These accounts have larger quota limits than the "standard_api" and, thus, this package may be useful for individuals seeking to submit large batch jobs within R to the Google Maps API. Placement also provides methods for accessing the standard API using a (free) Google API key (see: <https://developers.google.com/maps/documentation/javascript/get-api-key#get-an-api-key>).
License: MIT + file LICENSE
LazyData: TRUE
Imports: RCurl, jsonlite, base64enc, digest, urltools, stringi
URL: https://github.com/derekyves/placement
BugReports: https://github.com/derekyves/placement/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 21:59:44 UTC; ddarves
Repository: CRAN
Date/Publication: 2016-07-28 00:07:05

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Package neotoma updated to version 1.6.0 with previous version 1.5.1 dated 2016-05-06

Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (http://api.neotomadb.org/). The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>

Diff between neotoma versions 1.5.1 dated 2016-05-06 and 1.6.0 dated 2016-07-27

 DESCRIPTION                        |    8 +-
 MD5                                |   44 +++++++-------
 NAMESPACE                          |    6 +
 NEWS                               |    7 ++
 R/bind.R                           |   75 +++++++++++++-----------
 R/get_chroncontrol.R               |   12 +++
 R/get_closest.R                    |only
 R/get_contact.R                    |   15 ++--
 R/get_dataset.R                    |    4 -
 R/get_download.R                   |    8 +-
 R/get_geochron.R                   |   92 +++++++++++++++---------------
 R/get_table.R                      |   11 ++-
 R/print.geochronologic_list.R      |   11 ++-
 R/write_agefile.R                  |   55 ++++++++++--------
 README.md                          |   10 ---
 man/bind.Rd                        |   16 ++---
 man/get_chroncontrol.Rd            |   12 +++
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 man/get_geochron.Rd                |   16 ++---
 man/get_table.Rd                   |   10 ++-
 man/write_agefile.Rd               |   12 +++
 tests/testthat/test_examples.R     |    9 +-
 tests/testthat/test_neotoma.R      |  113 ++++++++++++++++++-------------------
 tests/testthat/test_simple_paper.R |    5 -
 24 files changed, 309 insertions(+), 242 deletions(-)

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New package MWLasso with initial version 1.3
Package: MWLasso
Type: Package
Title: Penalized Moving-Window Lasso Method for Genome-Wide Association Studies
Version: 1.3
Date: 2016-07-27
Author: Minli Bao
Maintainer: Minli Bao <minli-bao@uiowa.edu>
Description: The Moving-Window Lasso (MWLasso) method for genome-wide association studies. A window scans the design matrix. For predictors in the same window, their coefficients estimates are smoothed.
License: GPL
Packaged: 2016-07-27 19:48:18 UTC; Minli
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-07-27 23:50:35

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Package kyotil updated to version 2016.7-27 with previous version 2016.7-9 dated 2016-07-11

Title: Utility Functions by Youyi, Krisz and Others
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>

Diff between kyotil versions 2016.7-9 dated 2016-07-11 and 2016.7-27 dated 2016-07-27

 DESCRIPTION     |    8 +-
 MD5             |   14 +--
 NAMESPACE       |    4 -
 R/plotting.R    |   24 ++++--
 R/print.R       |  204 +++++++++++++++++++++++++++++++-------------------------
 R/random.R      |    4 -
 R/string.R      |   24 ------
 man/plotting.Rd |    6 +
 8 files changed, 151 insertions(+), 137 deletions(-)

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Package GLDEX updated to version 2.0.0.4 with previous version 2.0.0.3 dated 2015-07-04

Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su <allegro.su@gmail.com>

Diff between GLDEX versions 2.0.0.3 dated 2015-07-04 and 2.0.0.4 dated 2016-07-27

 DESCRIPTION                  |    8 ++++----
 MD5                          |   19 ++++++++++---------
 R/fun.diag.ks.g.R            |    4 ++--
 R/fun.diag.ks.g.bimodal.R    |    4 ++--
 R/fun.diag1.R                |    8 ++++----
 R/fun.diag2.R                |    8 ++++----
 README                       |only
 man/fun.diag.ks.g.Rd         |    5 +++--
 man/fun.diag.ks.g.bimodal.Rd |    5 +++--
 man/fun.diag1.Rd             |    5 +++--
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 11 files changed, 38 insertions(+), 33 deletions(-)

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Package etl updated to version 0.3.3 with previous version 0.3.1 dated 2016-06-13

Title: Extract-Transform-Load Framework for Medium Data
Description: A framework for loading medium-sized data from the Internet to a local or remote relational database management system. This package itself doesn't do much more than provide a toy example and set up the method structure. Packages that depend on this package will facilitate the construction and maintenance of their respective databases.
Author: Ben Baumer [aut, cre], Carson Sievert [ctb]
Maintainer: Ben Baumer <ben.baumer@gmail.com>

Diff between etl versions 0.3.1 dated 2016-06-13 and 0.3.3 dated 2016-07-27

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 etl-0.3.3/etl/NAMESPACE                         |   23 ++
 etl-0.3.3/etl/NEWS.md                           |   12 +
 etl-0.3.3/etl/R/etl.R                           |   40 ++++
 etl-0.3.3/etl/R/etl_create.R                    |   21 +-
 etl-0.3.3/etl/R/etl_load.R                      |  127 +++++++++++---
 etl-0.3.3/etl/R/etl_transform.R                 |   12 -
 etl-0.3.3/etl/R/utils.R                         |  205 +++++++++++++++---------
 etl-0.3.3/etl/README.md                         |   33 ++-
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 26 files changed, 478 insertions(+), 185 deletions(-)

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Package bibliometrix updated to version 1.0 with previous version 0.8 dated 2016-06-20

Title: Bibliometric and Co-Citation Analysis Tool
Description: Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from SCOPUS and Thomson Reuters' ISI Web of Knowledge databases, performing bibliometric analysis and building data matrices for co-citation, coupling and scientific collaboration analysis.
Author: Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>

Diff between bibliometrix versions 0.8 dated 2016-06-20 and 1.0 dated 2016-07-27

 DESCRIPTION                         |    8 -
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 NAMESPACE                           |  154 ++++++++++++++++++++++++++++++++----
 NEWS                                |   11 ++
 R/Hindex.R                          |    3 
 R/biblioAnalysis.R                  |    1 
 R/biblioNetwork.R                   |    3 
 R/citations.R                       |    1 
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 R/couplingSimilarity.R              |    1 
 R/dfMerge.R                         |    1 
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 R/isi2df.R                          |    1 
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 R/keywordsAssoc.R                   |    1 
 R/localCitations.R                  |    3 
 R/lotka.R                           |    3 
 R/metaTagExtraction.R               |    3 
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 R/scopus2df.R                       |    2 
 R/summary.bibliometrix.R            |    5 -
 R/tableTag.R                        |    1 
 R/timeslice.R                       |    3 
 R/trim.leading.R                    |    3 
 build/vignette.rds                  |binary
 inst/doc/bibliometrix-vignette.R    |   31 +++++--
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 inst/doc/bibliometrix-vignette.html |   70 ++++++++++++----
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 32 files changed, 502 insertions(+), 101 deletions(-)

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Package archivist updated to version 2.1 with previous version 2.0.4 dated 2016-05-12

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>

Diff between archivist versions 2.0.4 dated 2016-05-12 and 2.1 dated 2016-07-27

 DESCRIPTION              |    7 ++-
 MD5                      |   94 ++++++++++++++++++++++++-----------------------
 NAMESPACE                |    1 
 NEWS.md                  |   14 ++++++-
 R/addArchivistHooks.R    |   56 +++++++++++++++++-----------
 R/ahistory.R             |   21 ++++++++++
 R/archivist-package.R    |    5 ++
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 R/asearch.R              |   10 ++++-
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 R/loadFromRepo.R         |   10 ++++-
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 man/saveToRepo.Rd        |    3 +
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 man/setRepo.Rd           |    6 ++-
 man/shinySearchInRepo.Rd |    3 +
 man/showRepo.Rd          |    3 +
 man/splitTags.Rd         |    3 +
 man/summaryRepo.Rd       |    3 +
 man/zipRepo.Rd           |    6 ++-
 49 files changed, 366 insertions(+), 187 deletions(-)

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Package IsoplotR updated to version 0.6 with previous version 0.5 dated 2016-07-03

Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently 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 the 'York' approach. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Calculates 40A/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Future versions will include functionality for the Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, ternary diagrams, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app at http://isoplotr.london-geochron.com. Offline access to this interface will be provided at a later point in time.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 0.5 dated 2016-07-03 and 0.6 dated 2016-07-27

 DESCRIPTION         |    8 ++--
 MD5                 |   53 ++++++++++++++++--------------
 NAMESPACE           |   12 ++++++
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 R/age.R             |   48 ++++++++++++++++++++-------
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 R/io.R              |   23 ++++++++++++-
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 30 files changed, 530 insertions(+), 275 deletions(-)

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Permanent link

New package iDOS with initial version 1.0.0
Package: iDOS
Type: Package
Title: Integrated Discovery of Oncogenic Signatures
Version: 1.0.0
Date: 2016-07-27
Author: Syed Haider, Francesca M Buffa
Maintainer: Syed Haider <Syed.Haider@oncology.ox.ac.uk>
Depends: R (>= 2.15.0), VennDiagram (>= 1.6.5)
Description: Integrate molecular profiles to discover candidate oncogenic drivers.
License: GPL-2
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-07-27 17:31:11 UTC; shaider
Repository: CRAN
Date/Publication: 2016-07-27 20:25:35

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New package SimSCRPiecewise with initial version 0.1.0
Package: SimSCRPiecewise
Type: Package
Title: 'Simulates Univariate and Semi-Competing Risks Data Given Covariates and Piecewise Exponential Baseline Hazards'
Version: 0.1.0
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <Andrew.G.Chapple@rice.edu>
Description: Contains two functions for simulating survival data from piecewise exponential hazards with a proportional hazards adjustment for covariates. The first function SimUNIVPiecewise simulates univariate survival data based on a piecewise exponential hazard, covariate matrix and true regression vector. The second function SimSCRPiecewise semi-competing risks data based on three piecewise exponential hazards, three true regression vectors and three matrices of patient covariates (which can be different or the same). This simulates from the Semi-Markov model of Lee et al (2015) given patient covariates, regression parameters, patient frailties and baseline hazard functions.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-27 15:22:49 UTC; Andrew
Repository: CRAN
Date/Publication: 2016-07-27 19:03:16

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Package metricTester updated to version 1.3.0 with previous version 1.2.2 dated 2016-06-25

Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and performance of phylogenetic metrics and null models.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>

Diff between metricTester versions 1.2.2 dated 2016-06-25 and 1.3.0 dated 2016-07-27

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 metricTester-1.3.0/metricTester/R/FDis.R                                            |    2 
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 metricTester-1.3.0/metricTester/R/randomArena.R                                     |    4 
 metricTester-1.3.0/metricTester/R/readIn.R                                          |    4 
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 metricTester-1.3.0/metricTester/R/varyX.R                                           |    4 
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 metricTester-1.3.0/metricTester/man/arenaTest.Rd                                    |   25 
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 metricTester-1.3.0/metricTester/man/prepData.Rd                                     |    4 
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 metricTester-1.3.0/metricTester/man/randomArena.Rd                                  |    4 
 metricTester-1.3.0/metricTester/man/readIn.Rd                                       |    4 
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 metricTester-1.3.0/metricTester/man/summCorrs.Rd                                    |    4 
 metricTester-1.3.0/metricTester/man/summaries.Rd                                    |   15 
 metricTester-1.3.0/metricTester/man/traitField.Rd                                   |    6 
 metricTester-1.3.0/metricTester/man/varLandscape.Rd                                 |only
 metricTester-1.3.0/metricTester/man/varyX.Rd                                        |    4 
 metricTester-1.3.0/metricTester/tests/testthat/test_post_sim_analyses_by_both.R     |    8 
 metricTester-1.3.0/metricTester/tests/testthat/test_post_sim_analyses_by_richness.R |    8 
 143 files changed, 1805 insertions(+), 1017 deletions(-)

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Package maps updated to version 3.1.1 with previous version 3.1.0 dated 2016-02-13

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg. Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between maps versions 3.1.0 dated 2016-02-13 and 3.1.1 dated 2016-07-27

 DESCRIPTION           |    8 ++++----
 MD5                   |   18 +++++++++---------
 R/db.r                |    7 +++++--
 R/map.r               |    7 +++++--
 R/zzz.R               |    9 ---------
 README.md             |    4 ++--
 data/world.cities.rda |binary
 inst/NEWS.Rd          |    9 ++++++++-
 inst/README.md        |    4 ++--
 src/legacy_world.name |    4 ++--
 10 files changed, 37 insertions(+), 33 deletions(-)

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New package BayesPiecewiseICAR with initial version 0.1.0
Package: BayesPiecewiseICAR
Type: Package
Title: Hierarchical Bayesian Model for a Hazard Function
Version: 0.1.0
Author: person("Andrew", "Chapple", email = "Andrew.G.Chapple@rice.edu", role = c("aut", "cre"))
Maintainer: Andrew Chapple <Andrew.G.Chapple@rice.edu>
Description: Fits a piecewise exponential hazard to survival data using a Hierarchical Bayesian model with an Intrinsic Conditional Autoregressive formulation for the spatial dependency in the hazard rates for each piece. This function uses Metropolis- Hastings-Green MCMC to allow the number of split points to vary. This function outputs graphics that display the histogram of the number of split points and the trace plots of the hierarchical parameters. The function outputs a list that contains the posterior samples for the number of split points, the location of the split points, and the log hazard rates corresponding to these splits. Additionally, this outputs the posterior samples of the two hierarchical parameters, Mu and Sigma^2.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
Depends: mvtnorm
NeedsCompilation: no
Packaged: 2016-07-27 15:16:18 UTC; Andrew
Repository: CRAN
Date/Publication: 2016-07-27 19:00:54

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Package vipor updated to version 0.4.3 with previous version 0.4.2 dated 2016-07-03

Title: Plot Categorical Data Using Quasirandom Noise and Density Estimates
Description: Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Author: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>

Diff between vipor versions 0.4.2 dated 2016-07-03 and 0.4.3 dated 2016-07-27

 DESCRIPTION                    |    8 ++--
 MD5                            |   22 ++++++------
 R/violinPoint.R                |   12 +++---
 README.md                      |   41 ++++++++++++++++++++++-
 inst/doc/methodComparison.R    |   72 +++++++++++++++++++++--------------------
 inst/doc/methodComparison.Rnw  |   64 +++++++++++++++++++-----------------
 inst/doc/methodComparison.pdf  |binary
 inst/doc/usageExamples.Rnw     |    3 +
 inst/doc/usageExamples.pdf     |binary
 man/offsetX.Rd                 |    8 ++--
 vignettes/methodComparison.Rnw |   64 +++++++++++++++++++-----------------
 vignettes/usageExamples.Rnw    |    3 +
 12 files changed, 177 insertions(+), 120 deletions(-)

More information about vipor at CRAN
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