Tue, 31 May 2016

Package TAM updated to version 1.995-0 with previous version 1.99-6 dated 2016-04-15

Title: Test Analysis Modules
Description: Includes marginal maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models) and joint maximum likelihood estimation for models from the Rasch family. Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package MCI updated to version 1.0.2 with previous version 1.0.1 dated 2016-04-24

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. The functions in this package include fitting the MCI model, the log-centering transformation of MCI datasets and tools for data preparation.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>

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Package CDM updated to version 4.991-1 with previous version 4.8-0 dated 2016-03-10

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous data. This package enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the multidimensional linear compensatory item response model and the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package immer updated to version 0.5-0 with previous version 0.4-0 dated 2016-03-07

Title: Item Response Models for Multiple Ratings
Description: Implements some item response models for multiple ratings, including the hierarchical rater model, conditional maximum likelihood estimation of linear logistic partial credit model and a wrapper function to the commercial FACETS program.
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package VGAMdata updated to version 1.0-2 with previous version 1.0-0 dated 2015-10-29

Title: Data Supporting the 'VGAM' Package
Description: Data sets to accompany the VGAM package and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology).
Author: Thomas Yee [aut, cre, cph], James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

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Package robustbase updated to version 0.92-6 with previous version 0.92-5 dated 2015-07-22

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Original code by many authors, notably Peter Rousseeuw and Christophe Croux, see file 'Copyrights'; Valentin Todorov <valentin.todorov@chello.at>, Andreas Ruckstuhl <andreas.ruckstuhl@zhaw.ch>, Matias Salibian-Barrera <matias@stat.ubc.ca>, Tobias Verbeke <tobias.verbeke@openanalytics.eu>, Manuel Koller <mkoller@ispm.unibe.ch>, Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package pomp updated to version 1.5 with previous version 1.4.1.1 dated 2016-03-28

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a platform for the implementation of new inference methods.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb], Sebastian Funk [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

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Package PolyTrend updated to version 1.2 with previous version 1.1 dated 2016-05-12

Title: Trend Classification Algorithm
Description: This algorithm classifies the trends into linear, quadratic, cubic, concealed and no-trend types. The "concealed trends" are those trends that possess quadratic or cubic forms, but the net change from the start of the time period to the end of the time period hasn't been significant. The "no-trend" category includes simple linear trends with statistically in-significant slope coefficient.
Author: Sadegh Jamali, Hristo Tomov
Maintainer: Hristo Tomov <tomov.hristo@gmail.com>

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Package networkD3 updated to version 0.2.11 with previous version 0.2.10 dated 2016-04-12

Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.
Author: Christopher Gandrud [aut, cre], J.J. Allaire [aut], Kenton Russell [aut], B.W. Lewis [ctb], Kevin Kuo [ctb], Charles Sese [ctb], Peter Ellis [ctb], Jonathan Owen [ctb], Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

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Package mlVAR updated to version 0.3.0 with previous version 0.1.0 dated 2015-06-10

Title: Multi-Level Vector Autoregression
Description: Compute estimates of the multivariate vector autoregression model as introduced by Bringmann et al. (2013) which can be extended through treatment effects, covariates and pre- and post-assessment effects.
Author: Sacha Epskamp, Marie K. Deserno and Laura F. Bringmann
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package maSAE updated to version 0.1-5 with previous version 0.1-4 dated 2016-02-26

Title: Mandallaz' Model-Assisted Small Area Estimators
Description: An S4 implementation of the unbiased extension of the model- assisted synthetic-regression estimator proposed by Mandallaz (2013) <DOI:10.1139/cjfr-2012-0381>, Mandallaz et al. (2013) <DOI:10.1139/cjfr-2013-0181> and Mandallaz (2014) <DOI:10.1139/cjfr-2013-0449>. It yields smaller variances than the standard bias correction, the generalised regression estimator.
Author: Andreas Dominik Cullmann [aut, cre], Daniel Mandallaz [ctb], Alexander Francis Massey [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_masae@arcor.de>

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Package HandTill2001 updated to version 0.2-12 with previous version 0.2-11 dated 2016-02-24

Title: Multiple Class Area under ROC Curve
Description: An S4 implementation of Eq. (3) and Eq. (7) by David J. Hand and Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
Author: Andreas Dominik Cullmann [aut, cre], Edgar Kublin [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_handtill2001@arcor.de>

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Package Demerelate updated to version 0.9 with previous version 0.8-1 dated 2013-12-17

Title: Functions to Calculate Relatedness on Diploid Genetic Data
Description: Functions to calculate pairwise relatedness on diploid genetic datasets. Different estimators for relatedness can be combined with information on geographical distances. Information on heterozygosity, allele- and genotype diversity as well as genetic F-statistics are provided for each population.
Author: Philipp Kraemer [aut, cre], Gabriele Gerlach [aut]
Maintainer: Philipp Kraemer <Philipp.Kraemer@uni-oldenburg.de>

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Permanent link

Package strataG updated to version 1.0.5 with previous version 1.0.3 dated 2016-04-04

Title: Summaries and Population Structure Analyses of Genetic Data
Description: A toolkit for analyzing stratified population genetic data.
Author: Eric Archer [aut, cre], Paula Adams [aut], Brita Schneiders [aut]
Maintainer: Eric Archer <eric.archer@noaa.gov>

Diff between strataG versions 1.0.3 dated 2016-04-04 and 1.0.5 dated 2016-05-31

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More information about strataG at CRAN
Permanent link

Package rfPermute updated to version 2.0.1 with previous version 2.0 dated 2016-03-03

Title: Estimate Permutation p-Values for Random Forest Importance Metrics
Description: Estimate significance of importance metrics for a Random Forest model by permuting the response variable. Produces null distribution of importance metrics for each predictor variable and p-value of observed.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>

Diff between rfPermute versions 2.0 dated 2016-03-03 and 2.0.1 dated 2016-05-31

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Permanent link

Package iterpc updated to version 0.3.0 with previous version 0.2.9-1 dated 2016-04-20

Title: Efficient Iterator for Permutations and Combinations
Description: A collection of iterators for generating permutations and combinations with or without replacement; with distinct items or non-distinct items (multiset). The generated sequences are in lexicographical order (dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between iterpc versions 0.2.9-1 dated 2016-04-20 and 0.3.0 dated 2016-05-31

 DESCRIPTION                       |   15 +++---
 MD5                               |   34 +++++++-------
 NAMESPACE                         |    2 
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 README.md                         |    2 
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 tests/testthat/test-permutation.R |   35 ++++++++-------
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More information about iterpc at CRAN
Permanent link

Mon, 30 May 2016

Package sirt updated to version 1.11-0 with previous version 1.10-0 dated 2016-01-29

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R, including multidimensional compensatory and noncompensatory IRT models, MCMC for hierarchical IRT models and testlet models, NOHARM, Rasch copula model, faceted and hierarchical rater models, ordinal IRT model (ISOP), DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between sirt versions 1.10-0 dated 2016-01-29 and 1.11-0 dated 2016-05-30

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Package recmap updated to version 0.3.0 with previous version 0.2.1 dated 2016-05-02

Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2 construction heuristic (see 'citation("recmap")' for details). This algorithm draws maps according to a given statistical value (e. g. election results, population or epidemiological data). The basic idea of the RecMap algorithm is that each map region (e. g. different countries) is represented by a rectangle. The area of each rectangle represents the statistical value given as input (maintain zero cartographic error). Documentation about 'RecMap' is provided by a vignette included in this package and a 'RecMap gallery' site at <http://cartodraw.science/recmap/gallery>.
Author: Christian Panse
Maintainer: Christian Panse <Christian.Panse@gmail.com>

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Package mitml updated to version 0.3-2 with previous version 0.3-1 dated 2016-05-11

Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>

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Package Luminescence updated to version 0.6.0 with previous version 0.5.1 dated 2015-12-07

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut, trl, dtc], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Johannes Friedrich [aut], Norbert Mercier [aut], Rachel K. Smedley [aut], Julie Durcan [aut], Georgina King [aut], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>

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Package ClustMMDD updated to version 1.0.4 with previous version 1.0.3 dated 2016-02-21

Title: Variable Selection in Clustering by Mixture Models for Discrete Data
Description: An implementation of a variable selection procedure in clustering by mixture models for discrete data (clustMMDD). Genotype data are examples of such data with two unordered observations (alleles) at each locus for diploid individual. The two-fold problem of variable selection and clustering is seen as a model selection problem where competing models are characterized by the number of clusters K, and the subset S of clustering variables. Competing models are compared by penalized maximum likelihood criteria. We considered asymptotic criteria such as Akaike and Bayesian Information criteria, and a family of penalized criteria with penalty function to be data driven calibrated.
Author: Wilson Toussile
Maintainer: Wilson Toussile <wilson.toussile@gmail.com>

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Package eva updated to version 0.2.3 with previous version 0.2.2 dated 2016-05-02

Title: Extreme Value Analysis with Goodness-of-Fit Testing
Description: Goodness-of-fit tests for selection of r in the r-largest order statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the Generalized Pareto distribution (GPD). Random number generation and density functions for the GEVr distribution. Profile likelihood for return level estimation using the GEVr and Generalized Pareto distributions. P-value adjustments for sequential, multiple testing error control. Non-stationary fitting of GEVr and GPD, with availability for bootstrap based standard errors in the GEV1 setting to handle dependence.
Author: Brian Bader [aut, cre], Jun Yan [ctb]
Maintainer: Brian Bader <brianbader@mail.com>

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Package bfp updated to version 0.0-31 with previous version 0.0-30 dated 2016-03-09

Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms.
Author: Daniel Sabanes Bove <sabanesd@roche.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>

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Package wrassp updated to version 0.1.4 with previous version 0.1.3 dated 2014-12-01

Title: Interface to the ASSP Library
Description: A wrapper around Michel Scheffers's libassp (Advanced Speech Signal Processor). The libassp library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner.
Author: Raphael Winkelmann [aut, cre], Lasse Bombien [aut], Michel Scheffers [aut]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>

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Package stplanr updated to version 0.1.2 with previous version 0.1.1 dated 2016-01-16

Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning, including origin-destination analysis, route allocation and modelling travel patterns.
Author: Robin Lovelace [aut, cre], Richard Ellison [aut], Barry Rowlingson [aut] (Author of overline), Nick Bearman [aut] (Co-author of gclip)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package RItools updated to version 0.1-15 with previous version 0.1-13 dated 2016-01-17

Title: Randomization Inference Tools
Description: Tools for randomization inference.
Author: Jake Bowers <jwbowers@illinois.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, and Ben Hansen <ben.hansen@umich.edu>
Maintainer: Jake Bowers <jwbowers@illinois.edu>

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Package RForcecom updated to version 0.9 with previous version 0.8 dated 2015-10-26

Title: Data Integration Feature for Force.com and Salesforce.com
Description: Insert, update, retrieve, delete and bulk operate datasets with a SaaS based CRM Salesforce.com and a PaaS based application platform Force.com from R.
Author: Takekatsu Hiramura [aut, cre], Steven Mortimer [ctb], Alexis Iglauer [ctb]
Maintainer: Takekatsu Hiramura <thira@plavox.info>

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Package ParallelTree updated to version 0.1.1 with previous version 0.1.0 dated 2016-04-27

Title: Parallel Tree
Description: Provides two functions: Group_function() and Parallel_Tree(). Group_function() applies a given function (e.g.,mean()) to input variable(s) by group across levels. Has additional data management options. Parallel_Tree() uses 'ggplot2' to create a parallel coordinate plots (technically a facsimile of parallel coordinate plots in a Cartesian coordinate system). Used in combination these functions can create parallel tree plots, a variant of parallel coordinate plots, which are useful for visualizing multilevel data.
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>

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Package nmfgpu4R updated to version 0.2.5 with previous version 0.2.4 dated 2016-04-27

Title: Non-Negative Matrix Factorization (NMF) using CUDA
Description: Wrapper package for the nmfgpu library, which implements several Non-negative Matrix Factorization (NMF) algorithms for CUDA platforms. By using the acceleration of GPGPU computing, the NMF can be used for real-world problems inside the R environment. All CUDA devices starting with Kepler architecture are supported by the library.
Author: Sven Koitka [aut, cre, cph], Christoph M. Friedrich [ctb]
Maintainer: Sven Koitka <sven.koitka@fh-dortmund.de>

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Package likeLTD updated to version 6.1.0 with previous version 6.0.4 dated 2016-02-21

Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence. For further information see the likeLTD guide provided, or Balding, D.J. (2013) <DOI:10.1073/pnas.1219739110>.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>

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Package ggExtra updated to version 0.5 with previous version 0.4.0 dated 2016-03-28

Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main function is ggMarginal(), which can be used to add marginal histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

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Package geomnet updated to version 0.1.0 with previous version 0.0.1 dated 2015-12-30

Title: Network Visualization in the 'ggplot2' Framework
Description: Network visualization in the 'ggplot2' framework. Network functionality is provided in a single 'ggplot2' layer by calling the geom 'net'. Layouts are calculated using the 'sna' package, example networks are included.
Author: Samantha Tyner, Heike Hofmann
Maintainer: Samantha Tyner <sctyner@iastate.edu>

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Package bibliometrix updated to version 0.5 with previous version 0.3 dated 2016-05-21

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>

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Package basefun updated to version 0.0-32 with previous version 0.0-31 dated 2016-04-25

Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package iemiscdata updated to version 0.5.1 with previous version 0.5.0 dated 2016-02-04

Title: Irucka Embry's Miscellaneous Data Collection
Description: Miscellaneous data sets [Environmental/Water Resources Engineering].
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>

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Package iemisc updated to version 0.6.2 with previous version 0.5.1 dated 2016-05-18

Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions (Engineering Economics, Environmental/Water Resources Engineering, Geometry, Statistics, GNU Octave length functions, etc.).
Author: Irucka Embry [aut, cre]. Includes R source code and/or documentation previously published by: Felix Andrews (zoo) and Hans Werner Borchers (pracma). [Borrowed from DescTools description.]
Maintainer: Irucka Embry <iembry@ecoccs.com>

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Package CRF updated to version 0.3-9 with previous version 0.3-8 dated 2014-07-30

Title: Conditional Random Fields
Description: Implements modeling and computational tools for conditional random fields (CRF) model as well as other probabilistic undirected graphical models of discrete data with pairwise and unary potentials.
Author: Ling-Yun Wu [aut, cre]
Maintainer: Ling-Yun Wu <wulingyun@gmail.com>

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Package qwraps2 updated to version 0.2.1 with previous version 0.2.0 dated 2016-04-24

Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into '.Rnw' or '.Rmd' files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at <https://github.com/dewittpe/qwraps/>. The implementation and limited scope of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre], Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>

Diff between qwraps2 versions 0.2.0 dated 2016-04-24 and 0.2.1 dated 2016-05-30

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Package QICD updated to version 1.1.1 with previous version 1.0.1 dated 2016-02-29

Title: Estimate the Coefficients for Non-Convex Penalized Quantile Regression Model by using QICD Algorithm
Description: Extremely fast algorithm "QICD", Iterative Coordinate Descent Algorithm for High-dimensional Nonconvex Penalized Quantile Regression. This algorithm combines the coordinate descent algorithm in the inner iteration with the majorization minimization step in the outside step. For each inner univariate minimization problem, we only need to compute a one-dimensional weighted median, which ensures fast computation. Tuning parameter selection is based on two different method: the cross validation and BIC for quantile regression model. Details are described in the Peng,B and Wang,L. (2015) linked to via the URL below with <DOI:10.1080/10618600.2014.913516>.
Author: Bo Peng [aut, cre], Rondall E. Jones [ctb], John A. Wisniewski [ctb]
Maintainer: Bo Peng <peng0199@umn.edu>

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Sun, 29 May 2016

Package qrmtools updated to version 0.0-6 with previous version 0.0-5 dated 2016-02-13

Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from the book "Quantitative Risk Management: Concepts, Techniques and Tools". Furthermore, new developments and auxiliary functions for Quantitative Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

Diff between qrmtools versions 0.0-5 dated 2016-02-13 and 0.0-6 dated 2016-05-29

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Package pracma updated to version 1.9.3 with previous version 1.8.8 dated 2015-11-27

Title: Practical Numerical Math Functions
Description: Functions from numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

Diff between pracma versions 1.8.8 dated 2015-11-27 and 1.9.3 dated 2016-05-29

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Package BOIN updated to version 2.3 with previous version 2.2 dated 2016-04-22

Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials. The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>

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Package adagio updated to version 0.6.5 with previous version 0.6.3 dated 2015-12-06

Title: Discrete and Global Optimization Routines
Description: The R package 'adagio' will provide methods and algorithms for discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

Diff between adagio versions 0.6.3 dated 2015-12-06 and 0.6.5 dated 2016-05-29

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Package NNS updated to version 0.1.9 with previous version 0.1.6 dated 2016-05-11

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

Diff between NNS versions 0.1.6 dated 2016-05-11 and 0.1.9 dated 2016-05-29

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Package rbamtools updated to version 2.16.0 with previous version 2.14.3 dated 2016-02-07

Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

Diff between rbamtools versions 2.14.3 dated 2016-02-07 and 2.16.0 dated 2016-05-29

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Package quint updated to version 1.2.0 with previous version 1.0 dated 2013-11-08

Title: Qualitative Interaction Trees
Description: Grows a qualitative interaction tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm randomized controlled trial.
Author: Elise Dusseldorp [aut, cre, cph], Lisa Doove [aut], Jeanne van de Put [aut], Cor Ninaber [ctb] (supported with the plot function), Iven Van Mechelen [aut, cph]
Maintainer: Elise Dusseldorp <elise.dusseldorp@fsw.leidenuniv.nl>

Diff between quint versions 1.0 dated 2013-11-08 and 1.2.0 dated 2016-05-29

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Package MetaLandSim updated to version 0.5.2 with previous version 0.5.1 dated 2016-05-05

Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>

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Package evclust updated to version 1.0.2 with previous version 1.0.1 dated 2016-05-28

Title: Evidential Clustering
Description: Various clustering algorithms that produce a credal partition, i.e., a set of Dempster-Shafer mass functions representing the membership of objects to clusters. The mass functions quantify the cluster-membership uncertainty of the objects. The algorithms are: Evidential c-Means (ECM), Relational Evidential c-Means (RECM), Constrained Evidential c-Means (CECM), EVCLUS and EK-NNclus.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>

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Sat, 28 May 2016

Package CHNOSZ updated to version 1.0.8 with previous version 1.0.7 dated 2015-11-19

Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry and low-temperature geochemistry. The features include calculation of the standard molal thermodynamic properties and chemical affinities of reactions involving minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous species; amino acid group additivity for the standard molal thermodynamic properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state for aqueous species; construction of equilibrium activity diagrams as a function of temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>

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Package varbvs updated to version 2.0.0 with previous version 1.0 dated 2012-04-10

Title: Large-Scale Bayesian Variable Selection Using Variational Methods
Description: Fast algorithms for fitting Bayesian variable selection models and computing Bayes factors, in which the outcome (or response variable) is modeled using a linear regression or a logistic regression. The algorithms are based on the variational approximations described in "Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies" (P. Carbonetto & M. Stephens, 2012, <DOI:10.1214/12-BA703>). This software has been applied to large data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto, Matthew Stephens
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>

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Package itsadug updated to version 2.1 with previous version 2.0 dated 2016-03-20

Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).
Author: Jacolien van Rij [aut, cre], Martijn Wieling [aut], R. Harald Baayen [aut], Hedderik van Rijn [ctb]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>

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Package htmltab updated to version 0.7.0 with previous version 0.6.0 dated 2015-07-22

Title: Assemble Data Frames from HTML Tables
Description: HTML tables are a valuable data source but extracting and recasting these data into a useful format can be tedious. This package allows to collect structured information from HTML tables. It is similar to readHTMLTable() of the XML package but provides three major advantages. First, the function automatically expands row and column spans in the header and body cells. Second, users are given more control over the identification of header and body rows which will end up in the R table, including semantic header information that appear throughout the body. Third, the function preprocesses table code, corrects common types of malformations, removes unneeded parts and so helps to alleviate the need for tedious post-processing.
Author: Christian Rubba [aut, cre]
Maintainer: Christian Rubba <christian.rubba@gmail.com>

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Package rdrobust updated to version 0.91 with previous version 0.90 dated 2016-05-08

Title: Robust Data-Driven Statistical Inference in Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell, <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>

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Package MVar.pt updated to version 1.8 with previous version 1.7 dated 2016-04-14

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), analise de multiplos fatores (MFA), para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Fri, 27 May 2016

Package softclassval updated to version 1.0-20160527 with previous version 1.0-20150416 dated 2015-04-16

Title: Soft Classification Performance Measures
Description: An extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1].
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>

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Package arrayhelpers updated to version 1.0-20160527 with previous version 0.76-20120816 dated 2012-08-17

Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>

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Package BinNor updated to version 2.1 with previous version 2.0 dated 2012-05-24

Title: Simultaneous Generation of Multivariate Binary and Normal Variates
Description: Generating multiple binary and normal variables simultaneously given marginal characteristics and association structure based on the methodology proposed by Demirtas and Doganay (2012).
Author: Anup Amatya, Hakan Demirtas
Maintainer: Anup Amatya <aamatya@nmsu.edu>

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Package VGAM updated to version 1.0-2 with previous version 1.0-1 dated 2016-03-15

Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of statistical regression models. At the heart of it are the vector generalized linear and additive model (VGLM/VGAM) classes, and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and VGAM package. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

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Package TipDatingBeast updated to version 1.0-2 with previous version 0.1-6 dated 2015-07-29

Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for Phylogenetic Analysis)
Description: Assist performing tip-dating of phylogenetic trees with BEAST.
Author: Adrien Rieux, Camilo Khatchikian
Maintainer: Camilo Khatchikian <ckhatchikian@gmail.com>

Diff between TipDatingBeast versions 0.1-6 dated 2015-07-29 and 1.0-2 dated 2016-05-27

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More information about TipDatingBeast at CRAN
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Package stringi updated to version 1.1.1 with previous version 1.0-1 dated 2015-10-22

Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code); IBM and other contributors (ICU4C 55.1 source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between stringi versions 1.0-1 dated 2015-10-22 and 1.1.1 dated 2016-05-27

 DESCRIPTION                              |   17 
 INSTALL                                  |   10 
 LICENSE                                  |    6 
 MD5                                      |  541 +++++++++++++++----------------
 NAMESPACE                                |   10 
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 inst/CITATION                            |   11 
 man/oper_comparison.Rd                   |   41 --
 man/oper_plus.Rd                         |    3 
 man/stri_compare.Rd                      |   43 --
 man/stri_count.Rd                        |    8 
 man/stri_count_boundaries.Rd             |   73 ----
 man/stri_datetime_add.Rd                 |   18 -
 man/stri_datetime_create.Rd              |   17 
 man/stri_datetime_fields.Rd              |   17 
 man/stri_datetime_format.Rd              |   17 
 man/stri_datetime_fstr.Rd                |   17 
 man/stri_datetime_now.Rd                 |   16 
 man/stri_datetime_symbols.Rd             |   17 
 man/stri_detect.Rd                       |   33 -
 man/stri_dup.Rd                          |    6 
 man/stri_duplicated.Rd                   |   91 +----
 man/stri_enc_detect.Rd                   |   12 
 man/stri_enc_detect2.Rd                  |   54 ---
 man/stri_enc_fromutf32.Rd                |   12 
 man/stri_enc_info.Rd                     |    7 
 man/stri_enc_isascii.Rd                  |   12 
 man/stri_enc_isutf16.Rd                  |   10 
 man/stri_enc_isutf8.Rd                   |   12 
 man/stri_enc_list.Rd                     |    7 
 man/stri_enc_mark.Rd                     |    7 
 man/stri_enc_set.Rd                      |    6 
 man/stri_enc_toascii.Rd                  |   12 
 man/stri_enc_tonative.Rd                 |   12 
 man/stri_enc_toutf32.Rd                  |   12 
 man/stri_enc_toutf8.Rd                   |   14 
 man/stri_encode.Rd                       |   12 
 man/stri_escape_unicode.Rd               |    3 
 man/stri_extract.Rd                      |   19 -
 man/stri_extract_boundaries.Rd           |   85 ----
 man/stri_flatten.Rd                      |    7 
 man/stri_info.Rd                         |    2 
 man/stri_install.Rd                      |    3 
 man/stri_isempty.Rd                      |    7 
 man/stri_join.Rd                         |   22 -
 man/stri_join_list.Rd                    |only
 man/stri_length.Rd                       |    7 
 man/stri_list2matrix.Rd                  |    3 
 man/stri_locale_info.Rd                  |    8 
 man/stri_locale_list.Rd                  |    7 
 man/stri_locale_set.Rd                   |    6 
 man/stri_locate.Rd                       |   20 -
 man/stri_locate_boundaries.Rd            |   99 +----
 man/stri_match.Rd                        |   25 -
 man/stri_numbytes.Rd                     |    7 
 man/stri_opts_brkiter.Rd                 |   23 -
 man/stri_opts_collator.Rd                |   47 --
 man/stri_opts_fixed.Rd                   |    4 
 man/stri_opts_regex.Rd                   |    4 
 man/stri_order.Rd                        |   45 --
 man/stri_pad.Rd                          |    2 
 man/stri_rand_lipsum.Rd                  |    5 
 man/stri_rand_shuffle.Rd                 |    5 
 man/stri_rand_strings.Rd                 |    5 
 man/stri_read_lines.Rd                   |    4 
 man/stri_read_raw.Rd                     |    4 
 man/stri_replace.Rd                      |   14 
 man/stri_replace_na.Rd                   |   23 -
 man/stri_reverse.Rd                      |    3 
 man/stri_split.Rd                        |   11 
 man/stri_split_boundaries.Rd             |   80 +---
 man/stri_split_lines.Rd                  |   32 -
 man/stri_startsendswith.Rd               |   23 -
 man/stri_stats_general.Rd                |    3 
 man/stri_stats_latex.Rd                  |    3 
 man/stri_sub.Rd                          |   44 --
 man/stri_subset.Rd                       |   72 ++--
 man/stri_timezone_info.Rd                |   18 -
 man/stri_timezone_list.Rd                |   18 -
 man/stri_timezone_set.Rd                 |   20 -
 man/stri_trans_casemap.Rd                |   83 +---
 man/stri_trans_char.Rd                   |   19 -
 man/stri_trans_general.Rd                |   19 -
 man/stri_trans_list.Rd                   |   19 -
 man/stri_trans_nf.Rd                     |   13 
 man/stri_trim.Rd                         |   24 -
 man/stri_unescape_unicode.Rd             |    3 
 man/stri_unique.Rd                       |   46 --
 man/stri_width.Rd                        |    6 
 man/stri_wrap.Rd                         |   69 ---
 man/stri_write_lines.Rd                  |    4 
 man/stringi-arguments.Rd                 |   37 +-
 man/stringi-encoding.Rd                  |   53 +--
 man/stringi-locale.Rd                    |  104 ++---
 man/stringi-package.Rd                   |   41 +-
 man/stringi-search-boundaries.Rd         |   84 +---
 man/stringi-search-charclass.Rd          |   25 -
 man/stringi-search-coll.Rd               |   65 +--
 man/stringi-search-fixed.Rd              |   22 -
 man/stringi-search-regex.Rd              |   29 -
 man/stringi-search.Rd                    |  166 +--------
 src/stri_ICU_settings.cpp                |    2 
 src/stri_TODO_justify.cpp                |    2 
 src/stri_TODO_splitpos.cpp               |    2 
 src/stri_TODO_uchar.cpp                  |    2 
 src/stri_brkiter.cpp                     |    2 
 src/stri_brkiter.h                       |    2 
 src/stri_bytesearch_matcher.h            |    2 
 src/stri_collator.cpp                    |    2 
 src/stri_common.cpp                      |    2 
 src/stri_compare.cpp                     |    2 
 src/stri_container_base.cpp              |    2 
 src/stri_container_base.h                |    2 
 src/stri_container_bytesearch.cpp        |    2 
 src/stri_container_bytesearch.h          |    2 
 src/stri_container_charclass.h           |    2 
 src/stri_container_double.h              |    2 
 src/stri_container_integer.h             |    2 
 src/stri_container_listint.cpp           |    2 
 src/stri_container_listint.h             |    2 
 src/stri_container_listraw.cpp           |    2 
 src/stri_container_listraw.h             |    2 
 src/stri_container_listutf8.cpp          |    2 
 src/stri_container_listutf8.h            |    2 
 src/stri_container_logical.h             |    2 
 src/stri_container_regex.cpp             |    2 
 src/stri_container_regex.h               |    2 
 src/stri_container_usearch.cpp           |    2 
 src/stri_container_usearch.h             |    2 
 src/stri_container_utf16.cpp             |    2 
 src/stri_container_utf16.h               |    2 
 src/stri_container_utf8.cpp              |    2 
 src/stri_container_utf8.h                |    2 
 src/stri_container_utf8_indexable.cpp    |    2 
 src/stri_container_utf8_indexable.h      |    2 
 src/stri_encoding_conversion.cpp         |    2 
 src/stri_encoding_detection.cpp          |    2 
 src/stri_encoding_management.cpp         |    2 
 src/stri_escape.cpp                      |    2 
 src/stri_exception.cpp                   |    2 
 src/stri_exception.h                     |    2 
 src/stri_exports.h                       |   30 -
 src/stri_external.h                      |    2 
 src/stri_interval.h                      |    2 
 src/stri_intvec.h                        |    2 
 src/stri_join.cpp                        |   50 ++
 src/stri_length.cpp                      |    2 
 src/stri_macros.h                        |   12 
 src/stri_messages.h                      |    7 
 src/stri_pad.cpp                         |    2 
 src/stri_prepare_arg.cpp                 |    2 
 src/stri_random.cpp                      |    2 
 src/stri_reverse.cpp                     |    2 
 src/stri_search_boundaries_count.cpp     |    2 
 src/stri_search_boundaries_extract.cpp   |    2 
 src/stri_search_boundaries_locate.cpp    |    2 
 src/stri_search_boundaries_split.cpp     |    2 
 src/stri_search_class_count.cpp          |    2 
 src/stri_search_class_detect.cpp         |    9 
 src/stri_search_class_extract.cpp        |    2 
 src/stri_search_class_locate.cpp         |    2 
 src/stri_search_class_replace.cpp        |   32 +
 src/stri_search_class_split.cpp          |    2 
 src/stri_search_class_startsendswith.cpp |    2 
 src/stri_search_class_subset.cpp         |   84 ++++
 src/stri_search_class_trim.cpp           |    2 
 src/stri_search_coll_count.cpp           |    2 
 src/stri_search_coll_detect.cpp          |   11 
 src/stri_search_coll_extract.cpp         |    2 
 src/stri_search_coll_locate.cpp          |    2 
 src/stri_search_coll_replace.cpp         |   30 +
 src/stri_search_coll_split.cpp           |    2 
 src/stri_search_coll_startsendswith.cpp  |    2 
 src/stri_search_coll_subset.cpp          |   80 ++++
 src/stri_search_common.cpp               |    2 
 src/stri_search_fixed_count.cpp          |    2 
 src/stri_search_fixed_detect.cpp         |   11 
 src/stri_search_fixed_extract.cpp        |    2 
 src/stri_search_fixed_locate.cpp         |    2 
 src/stri_search_fixed_replace.cpp        |   27 +
 src/stri_search_fixed_split.cpp          |    2 
 src/stri_search_fixed_startsendswith.cpp |    2 
 src/stri_search_fixed_subset.cpp         |   73 ++++
 src/stri_search_in.cpp                   |    2 
 src/stri_search_other_replace.cpp        |    2 
 src/stri_search_other_split.cpp          |    2 
 src/stri_search_regex_count.cpp          |    9 
 src/stri_search_regex_detect.cpp         |   16 
 src/stri_search_regex_extract.cpp        |   17 
 src/stri_search_regex_locate.cpp         |   15 
 src/stri_search_regex_match.cpp          |   19 -
 src/stri_search_regex_replace.cpp        |   34 +
 src/stri_search_regex_split.cpp          |    2 
 src/stri_search_regex_subset.cpp         |   93 +++++
 src/stri_sort.cpp                        |    2 
 src/stri_stats.cpp                       |    2 
 src/stri_string8.h                       |    8 
 src/stri_string8buf.h                    |    2 
 src/stri_stringi.cpp                     |  363 ++++++++++----------
 src/stri_stringi.h                       |    2 
 src/stri_sub.cpp                         |   33 +
 src/stri_test.cpp                        |    2 
 src/stri_time_calendar.cpp               |    2 
 src/stri_time_format.cpp                 |    2 
 src/stri_time_symbols.cpp                |    2 
 src/stri_time_zone.cpp                   |    2 
 src/stri_trans_casemap.cpp               |    2 
 src/stri_trans_normalization.cpp         |    2 
 src/stri_trans_other.cpp                 |    2 
 src/stri_trans_transliterate.cpp         |    2 
 src/stri_ucnv.cpp                        |    2 
 src/stri_ucnv.h                          |    2 
 src/stri_uloc.cpp                        |    2 
 src/stri_utils.cpp                       |    2 
 src/stri_wrap.cpp                        |    2 
 272 files changed, 2268 insertions(+), 2476 deletions(-)

More information about stringi at CRAN
Permanent link

Package RcppArmadillo updated to version 0.7.100.3.0 with previous version 0.6.700.6.0 dated 2016-05-05

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.6.700.6.0 dated 2016-05-05 and 0.7.100.3.0 dated 2016-05-27

 ChangeLog                                                         |   25 
 DESCRIPTION                                                       |    8 
 MD5                                                               |  392 
 configure                                                         | 3934 +++++++++-
 configure.ac                                                      |only
 inst/NEWS.Rd                                                      |   20 
 inst/doc/RcppArmadillo-intro.pdf                                  |binary
 inst/doc/RcppArmadillo-unitTests.pdf                              |binary
 inst/include/RcppArmadilloLapack.h.in                             |    6 
 inst/include/armadillo                                            |   46 
 inst/include/armadillo_bits/Cube_bones.hpp                        |    6 
 inst/include/armadillo_bits/Cube_meat.hpp                         |   68 
 inst/include/armadillo_bits/GenCube_bones.hpp                     |    4 
 inst/include/armadillo_bits/Gen_bones.hpp                         |    4 
 inst/include/armadillo_bits/Mat_meat.hpp                          |    8 
 inst/include/armadillo_bits/Proxy.hpp                             |  242 
 inst/include/armadillo_bits/ProxyCube.hpp                         |   38 
 inst/include/armadillo_bits/SpMat_bones.hpp                       |    2 
 inst/include/armadillo_bits/SpMat_meat.hpp                        |   12 
 inst/include/armadillo_bits/SpProxy.hpp                           |   28 
 inst/include/armadillo_bits/arma_cmath.hpp                        |   12 
 inst/include/armadillo_bits/arma_config.hpp                       |    9 
 inst/include/armadillo_bits/arma_rng.hpp                          |    1 
 inst/include/armadillo_bits/arma_version.hpp                      |    8 
 inst/include/armadillo_bits/auxlib_meat.hpp                       |   98 
 inst/include/armadillo_bits/compiler_setup.hpp                    |  104 
 inst/include/armadillo_bits/config.hpp                            |   14 
 inst/include/armadillo_bits/config.hpp.cmake                      |   14 
 inst/include/armadillo_bits/debug.hpp                             |  123 
 inst/include/armadillo_bits/def_lapack.hpp                        |   72 
 inst/include/armadillo_bits/def_superlu.hpp                       |    8 
 inst/include/armadillo_bits/diagmat_proxy.hpp                     |    6 
 inst/include/armadillo_bits/diagview_meat.hpp                     |   12 
 inst/include/armadillo_bits/diskio_meat.hpp                       |    8 
 inst/include/armadillo_bits/eGlueCube_bones.hpp                   |    6 
 inst/include/armadillo_bits/eGlue_bones.hpp                       |    8 
 inst/include/armadillo_bits/eOpCube_bones.hpp                     |    6 
 inst/include/armadillo_bits/eOp_bones.hpp                         |    8 
 inst/include/armadillo_bits/eglue_core_meat.hpp                   |   42 
 inst/include/armadillo_bits/eop_aux.hpp                           |   40 
 inst/include/armadillo_bits/eop_core_bones.hpp                    |    3 
 inst/include/armadillo_bits/eop_core_meat.hpp                     |   31 
 inst/include/armadillo_bits/fn_accu.hpp                           |   22 
 inst/include/armadillo_bits/fn_all.hpp                            |    9 
 inst/include/armadillo_bits/fn_any.hpp                            |    9 
 inst/include/armadillo_bits/fn_approx_equal.hpp                   |    4 
 inst/include/armadillo_bits/fn_as_scalar.hpp                      |   27 
 inst/include/armadillo_bits/fn_chol.hpp                           |    3 
 inst/include/armadillo_bits/fn_clamp.hpp                          |    2 
 inst/include/armadillo_bits/fn_conv.hpp                           |    2 
 inst/include/armadillo_bits/fn_conv_to.hpp                        |   32 
 inst/include/armadillo_bits/fn_cor.hpp                            |    4 
 inst/include/armadillo_bits/fn_cov.hpp                            |    4 
 inst/include/armadillo_bits/fn_cross.hpp                          |    3 
 inst/include/armadillo_bits/fn_cumprod.hpp                        |    6 
 inst/include/armadillo_bits/fn_cumsum.hpp                         |    6 
 inst/include/armadillo_bits/fn_det.hpp                            |   16 
 inst/include/armadillo_bits/fn_diagmat.hpp                        |    6 
 inst/include/armadillo_bits/fn_diagvec.hpp                        |    3 
 inst/include/armadillo_bits/fn_diff.hpp                           |    4 
 inst/include/armadillo_bits/fn_dot.hpp                            |   20 
 inst/include/armadillo_bits/fn_eig_gen.hpp                        |    3 
 inst/include/armadillo_bits/fn_eig_pair.hpp                       |    3 
 inst/include/armadillo_bits/fn_eig_sym.hpp                        |    5 
 inst/include/armadillo_bits/fn_eigs_gen.hpp                       |    5 
 inst/include/armadillo_bits/fn_eigs_sym.hpp                       |    5 
 inst/include/armadillo_bits/fn_elem.hpp                           |  143 
 inst/include/armadillo_bits/fn_eps.hpp                            |   21 
 inst/include/armadillo_bits/fn_expmat.hpp                         |    3 
 inst/include/armadillo_bits/fn_eye.hpp                            |    8 
 inst/include/armadillo_bits/fn_fft.hpp                            |    8 
 inst/include/armadillo_bits/fn_fft2.hpp                           |    6 
 inst/include/armadillo_bits/fn_find.hpp                           |   12 
 inst/include/armadillo_bits/fn_find_unique.hpp                    |    4 
 inst/include/armadillo_bits/fn_flip.hpp                           |    4 
 inst/include/armadillo_bits/fn_hist.hpp                           |    5 
 inst/include/armadillo_bits/fn_histc.hpp                          |    4 
 inst/include/armadillo_bits/fn_inv.hpp                            |    9 
 inst/include/armadillo_bits/fn_join.hpp                           |   14 
 inst/include/armadillo_bits/fn_kmeans.hpp                         |   10 
 inst/include/armadillo_bits/fn_kron.hpp                           |   13 
 inst/include/armadillo_bits/fn_logmat.hpp                         |    2 
 inst/include/armadillo_bits/fn_max.hpp                            |   30 
 inst/include/armadillo_bits/fn_mean.hpp                           |   21 
 inst/include/armadillo_bits/fn_median.hpp                         |    8 
 inst/include/armadillo_bits/fn_min.hpp                            |   29 
 inst/include/armadillo_bits/fn_misc.hpp                           |   26 
 inst/include/armadillo_bits/fn_nonzeros.hpp                       |    4 
 inst/include/armadillo_bits/fn_norm.hpp                           |   12 
 inst/include/armadillo_bits/fn_normalise.hpp                      |    4 
 inst/include/armadillo_bits/fn_numel.hpp                          |    7 
 inst/include/armadillo_bits/fn_ones.hpp                           |   12 
 inst/include/armadillo_bits/fn_pinv.hpp                           |    3 
 inst/include/armadillo_bits/fn_princomp.hpp                       |    3 
 inst/include/armadillo_bits/fn_prod.hpp                           |   15 
 inst/include/armadillo_bits/fn_randg.hpp                          |   16 
 inst/include/armadillo_bits/fn_randi.hpp                          |   12 
 inst/include/armadillo_bits/fn_randn.hpp                          |   12 
 inst/include/armadillo_bits/fn_randu.hpp                          |   14 
 inst/include/armadillo_bits/fn_rank.hpp                           |    6 
 inst/include/armadillo_bits/fn_regspace.hpp                       |    3 
 inst/include/armadillo_bits/fn_repmat.hpp                         |    4 
 inst/include/armadillo_bits/fn_schur.hpp                          |    5 
 inst/include/armadillo_bits/fn_shift.hpp                          |    2 
 inst/include/armadillo_bits/fn_shuffle.hpp                        |    4 
 inst/include/armadillo_bits/fn_size.hpp                           |   14 
 inst/include/armadillo_bits/fn_solve.hpp                          |    8 
 inst/include/armadillo_bits/fn_sort.hpp                           |    6 
 inst/include/armadillo_bits/fn_sort_index.hpp                     |    6 
 inst/include/armadillo_bits/fn_speye.hpp                          |    6 
 inst/include/armadillo_bits/fn_spones.hpp                         |    3 
 inst/include/armadillo_bits/fn_sprandn.hpp                        |    7 
 inst/include/armadillo_bits/fn_sprandu.hpp                        |    7 
 inst/include/armadillo_bits/fn_spsolve.hpp                        |    3 
 inst/include/armadillo_bits/fn_sqrtmat.hpp                        |    2 
 inst/include/armadillo_bits/fn_stddev.hpp                         |    8 
 inst/include/armadillo_bits/fn_strans.hpp                         |    6 
 inst/include/armadillo_bits/fn_sum.hpp                            |   29 
 inst/include/armadillo_bits/fn_svd.hpp                            |    5 
 inst/include/armadillo_bits/fn_svds.hpp                           |   14 
 inst/include/armadillo_bits/fn_syl_lyap.hpp                       |    5 
 inst/include/armadillo_bits/fn_symmat.hpp                         |    6 
 inst/include/armadillo_bits/fn_toeplitz.hpp                       |   11 
 inst/include/armadillo_bits/fn_trace.hpp                          |   10 
 inst/include/armadillo_bits/fn_trans.hpp                          |    9 
 inst/include/armadillo_bits/fn_trapz.hpp                          |    2 
 inst/include/armadillo_bits/fn_trig.hpp                           |   26 
 inst/include/armadillo_bits/fn_trimat.hpp                         |    4 
 inst/include/armadillo_bits/fn_trunc_exp.hpp                      |    6 
 inst/include/armadillo_bits/fn_trunc_log.hpp                      |    5 
 inst/include/armadillo_bits/fn_unique.hpp                         |    3 
 inst/include/armadillo_bits/fn_var.hpp                            |   11 
 inst/include/armadillo_bits/fn_vectorise.hpp                      |    5 
 inst/include/armadillo_bits/fn_zeros.hpp                          |   14 
 inst/include/armadillo_bits/glue_cross_meat.hpp                   |    4 
 inst/include/armadillo_bits/glue_max_meat.hpp                     |   10 
 inst/include/armadillo_bits/glue_min_meat.hpp                     |    8 
 inst/include/armadillo_bits/glue_mixed_meat.hpp                   |   34 
 inst/include/armadillo_bits/glue_relational_meat.hpp              |   10 
 inst/include/armadillo_bits/glue_solve_meat.hpp                   |    4 
 inst/include/armadillo_bits/glue_times_meat.hpp                   |    6 
 inst/include/armadillo_bits/include_superlu.hpp                   |   99 
 inst/include/armadillo_bits/newarp_DenseGenMatProd_bones.hpp      |only
 inst/include/armadillo_bits/newarp_DenseGenMatProd_meat.hpp       |only
 inst/include/armadillo_bits/newarp_DoubleShiftQR_bones.hpp        |only
 inst/include/armadillo_bits/newarp_DoubleShiftQR_meat.hpp         |only
 inst/include/armadillo_bits/newarp_EigsSelect.hpp                 |only
 inst/include/armadillo_bits/newarp_GenEigsSolver_bones.hpp        |only
 inst/include/armadillo_bits/newarp_GenEigsSolver_meat.hpp         |only
 inst/include/armadillo_bits/newarp_SortEigenvalue.hpp             |only
 inst/include/armadillo_bits/newarp_SparseGenMatProd_bones.hpp     |only
 inst/include/armadillo_bits/newarp_SparseGenMatProd_meat.hpp      |only
 inst/include/armadillo_bits/newarp_SymEigsSolver_bones.hpp        |only
 inst/include/armadillo_bits/newarp_SymEigsSolver_meat.hpp         |only
 inst/include/armadillo_bits/newarp_TridiagEigen_bones.hpp         |only
 inst/include/armadillo_bits/newarp_TridiagEigen_meat.hpp          |only
 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_bones.hpp |only
 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp  |only
 inst/include/armadillo_bits/newarp_UpperHessenbergQR_bones.hpp    |only
 inst/include/armadillo_bits/newarp_UpperHessenbergQR_meat.hpp     |only
 inst/include/armadillo_bits/newarp_cx_attrib.hpp                  |only
 inst/include/armadillo_bits/op_all_meat.hpp                       |   10 
 inst/include/armadillo_bits/op_any_meat.hpp                       |   10 
 inst/include/armadillo_bits/op_chol_meat.hpp                      |    2 
 inst/include/armadillo_bits/op_clamp_meat.hpp                     |    4 
 inst/include/armadillo_bits/op_cx_scalar_meat.hpp                 |   26 
 inst/include/armadillo_bits/op_diagmat_meat.hpp                   |    8 
 inst/include/armadillo_bits/op_dot_meat.hpp                       |   10 
 inst/include/armadillo_bits/op_fft_meat.hpp                       |    6 
 inst/include/armadillo_bits/op_find_meat.hpp                      |   12 
 inst/include/armadillo_bits/op_find_unique_meat.hpp               |    4 
 inst/include/armadillo_bits/op_htrans_meat.hpp                    |    6 
 inst/include/armadillo_bits/op_inv_meat.hpp                       |    8 
 inst/include/armadillo_bits/op_logmat_meat.hpp                    |    4 
 inst/include/armadillo_bits/op_max_meat.hpp                       |   12 
 inst/include/armadillo_bits/op_median_meat.hpp                    |   10 
 inst/include/armadillo_bits/op_min_meat.hpp                       |   18 
 inst/include/armadillo_bits/op_misc_meat.hpp                      |   18 
 inst/include/armadillo_bits/op_nonzeros_meat.hpp                  |    4 
 inst/include/armadillo_bits/op_norm_meat.hpp                      |   18 
 inst/include/armadillo_bits/op_pinv_meat.hpp                      |    2 
 inst/include/armadillo_bits/op_princomp_meat.hpp                  |    2 
 inst/include/armadillo_bits/op_prod_meat.hpp                      |    4 
 inst/include/armadillo_bits/op_relational_meat.hpp                |   10 
 inst/include/armadillo_bits/op_reshape_meat.hpp                   |    6 
 inst/include/armadillo_bits/op_sort_index_meat.hpp                |    6 
 inst/include/armadillo_bits/op_strans_meat.hpp                    |    6 
 inst/include/armadillo_bits/op_unique_meat.hpp                    |    6 
 inst/include/armadillo_bits/op_vectorise_meat.hpp                 |    6 
 inst/include/armadillo_bits/podarray_meat.hpp                     |    4 
 inst/include/armadillo_bits/sp_auxlib_bones.hpp                   |   17 
 inst/include/armadillo_bits/sp_auxlib_meat.hpp                    |  352 
 inst/include/armadillo_bits/spdiagview_meat.hpp                   |   22 
 inst/include/armadillo_bits/spop_max_meat.hpp                     |   19 
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Package penalized updated to version 0.9-47 with previous version 0.9-46 dated 2016-04-18

Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>

Diff between penalized versions 0.9-46 dated 2016-04-18 and 0.9-47 dated 2016-05-27

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Package oglmx updated to version 2.0.0.0 with previous version 1.0.3 dated 2015-07-31

Title: Estimation of Ordered Generalized Linear Models
Description: Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased. This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects. Wrapper functions to estimate the standard limited dependent variable models are also included.
Author: Nathan Carroll
Maintainer: Nathan Carroll <nathan.carroll@ur.de>

Diff between oglmx versions 1.0.3 dated 2015-07-31 and 2.0.0.0 dated 2016-05-27

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Package glmmLasso updated to version 1.4.4 with previous version 1.4.3 dated 2016-04-28

Title: Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>

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Package clusterCrit updated to version 1.2.7 with previous version 1.2.6 dated 2015-08-31

Title: Clustering Indices
Description: Compute clustering validation indices.
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>

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Package Compositional updated to version 1.3 with previous version 1.2 dated 2016-04-01

Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

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Package SpatPCA updated to version 1.1.1.1 with previous version 1.1.1.0 dated 2016-02-11

Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>

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Package PoisBinOrdNonNor updated to version 1.1 with previous version 1.0 dated 2015-05-17

Title: Generation of Up to Four Different Types of Variables
Description: Generation of a chosen number of count, binary, ordinal, and continuous (via Fleishman polynomials) random variables, with specified correlations and marginal properties.
Author: Hakan Demirtas, Rachel Nordgren, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>

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Thu, 26 May 2016

Package texmexseq updated to version 0.2 with previous version 0.1 dated 2015-03-11

Title: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>

Diff between texmexseq versions 0.1 dated 2015-03-11 and 0.2 dated 2016-05-26

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Package spfrontier updated to version 0.2.3 with previous version 0.1.12 dated 2014-12-21

Title: Spatial Stochastic Frontier Models
Description: A set of tools for estimation of various spatial specifications of stochastic frontier models.
Author: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>
Maintainer: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>

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Package PST updated to version 0.88 with previous version 0.86 dated 2015-02-18

Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho <alexis.gabadinho@unige.ch>

Diff between PST versions 0.86 dated 2015-02-18 and 0.88 dated 2016-05-26

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Package HTSCluster updated to version 2.0.8 with previous version 2.0.4 dated 2014-08-26

Title: Clustering High-Throughput Transcriptome Sequencing (HTS) Data
Description: A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis- Rabusseau
Maintainer: Andrea Rau <andrea.rau@jouy.inra.fr>

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Package DiversityOccupancy updated to version 1.0.4 with previous version 1.0.3 dated 2016-05-12

Title: Building Diversity Models from Multiple Species Occupancy Models
Description: Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Author: Derek Corcoran [aut, cre], Dylan Kesler [aut], Nicole Michel [ctb], Mike Meredith [ctb]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>

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Package vcfR updated to version 1.1.0 with previous version 1.0.0 dated 2016-02-22

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

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Package unfoldr updated to version 0.5.5 with previous version 0.5.1 dated 2016-05-04

Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in the estimation of the joint size-shape-orientation distribution of spheroidal shaped particles based on the same measured quantities of corresponding planar section profiles. A single trivariate discretized version of the (stereological) integral equation in the case of prolate and oblate spheroids is solved numerically by the EM algorithm. The estimation of diameter distribution of spheres from planar sections (Wicksell's corpuscle problem) is also implemented. Further, the package provides routines for the simulation of a Poisson germ- grain process with either spheroids, spherocylinders or spheres as grains together with functions for planar sections. For the purpose of exact simulation a bivariate size-shape distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

Diff between unfoldr versions 0.5.1 dated 2016-05-04 and 0.5.5 dated 2016-05-26

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Package Qtools updated to version 1.1 with previous version 1.0 dated 2016-02-04

Title: Utilities for Quantiles
Description: This is a collection of functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, and restricted quantile regression.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>

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Package rfoaas updated to version 0.1.9 with previous version 0.1.8 dated 2015-10-24

Title: R Interface to 'FOAAS'
Description: R access to the 'FOAAS' (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package inctools updated to version 1.0.5 with previous version 1.0.3 dated 2016-05-18

Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross- sectional surveys and for calibrating tests for recent infection.
Author: Alex Welte [aut], Eduard Grebe [cre, aut], Avery McIntosh [aut], Petra Bäumler [aut], Reshma Kassanjee [ctb], Hilmarie Brand [ctb], Cari Van Schalkwyk [ctb], Yuruo Li [ctb], Simon Daniel [ctb], Stefano Ongarello [ctb], Yusuke Asai [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>

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Package imputeMulti updated to version 0.4.6 with previous version 0.4.5 dated 2016-05-05

Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

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Package Haplin updated to version 6.0.1 with previous version 6.0 dated 2016-05-25

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>

Diff between Haplin versions 6.0 dated 2016-05-25 and 6.0.1 dated 2016-05-26

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Package ecospat updated to version 2.0 with previous version 1.1 dated 2015-03-06

Title: Spatial Ecology Miscellaneous Methods
Description: Colection of R functions and data sets for the support of spatial ecology analyses with a focus on pre-, core and post- modelling analyses of species distribution, niche quantification and community assembly., written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann [aut], Valeria Di Cola [cre, aut], Blaise Petitpierre [ctb], Frank Breiner [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb], Robin Engler [ctb], Wim Hordijk [ctb], Julien Pottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb], Dorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis [ctb], Daniel Scherrer [ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte Ndiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb], Antoine Guisan [aut]
Maintainer: Valeria Di Cola <valeria.dicola@unil.ch>

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Package ddst updated to version 1.4 with previous version 1.03 dated 2012-08-19

Title: Data Driven Smooth Tests
Description: Smooth testing of goodness of fit. These tests are data driven (alternative hypothesis is dynamically selected based on data). In this package you will find various tests for exponent, Gaussian, Gumbel and uniform distribution.
Author: Przemyslaw Biecek (R code), Teresa Ledwina (support, descriptions)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between ddst versions 1.03 dated 2012-08-19 and 1.4 dated 2016-05-26

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Package climtrends updated to version 1.0.6 with previous version 1.0.5 dated 2015-09-20

Title: Statistical Methods for Climate Sciences
Description: Absolute homogeneity tests SNHT absolute 1-breaks, 1-break, SD different from 1, 2-breaks, Buishand, Pettitt, von Neumann ratio and ratio-rank, Worsley, and Craddock, Relative homogeneity tests SNHT absolute 1-breaks, 1-break SD different from 1, 2-breaks, Peterson and Easterling, and Vincent, Differences in scale between two groups Siegel–Tukey, Create reference time series mean, weights/correlation, finding outliers Grubbs, ESD, MAD, Tietjen Moore, Hampel, etc.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>

Diff between climtrends versions 1.0.5 dated 2015-09-20 and 1.0.6 dated 2016-05-26

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Package AnalyzeTS updated to version 1.9 with previous version 1.8 dated 2016-04-04

Title: Analyze Time Series
Description: Main function of package is helped to analyze time series, peculiar is fuzzy time series. The package can calculate AIC value of common time series models and propose the best models according AIC values. To fuzzy time series by "Chen", "Sing", "Heuristic" and "Chen-Hsu" models, also can fuzzy and forecast time series by Abbasov-Mamedova model.
Author: Tran Thi Ngoc Han <tranthingochan01011994@gmail.com>_ Doan Hai Nghi <Hainghi1426262609121094@gmail.com> _ Mai Thi Hong Diem <maidiemks@gmail.com> _ Nguyen Thi Diem My <myntdhg@gmail.com> _ Hong Viet Minh <hongvietminh@gmail.com> _ Vo Van Tai <vvtai@ctu.edu.vn>
Maintainer: Hong Viet Minh <hongvietminh@gmail.com>

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Package replicationInterval updated to version 2.0.1 with previous version 1.0.0 dated 2015-07-07

Title: Replication Interval Functions
Description: A common problem faced by journal reviewers and authors is the question of whether the results of a replication study are consistent with the original published study. One solution to this problem is to examine the effect size from the original study and generate the range of effect sizes that could reasonably be obtained (due to random sampling) in a replication attempt (i.e., calculate a replication interval). If a replication effect size falls outside the replication interval, then that effect likely did not occur due to the effects of sampling error alone. Alternatively, if a replication effect size falls within the replication interval, then the replication effect could have reasonably occurred due to the effects of sampling error alone. This package has functions that calculate the replication interval for the correlation (i.e., r), standardized mean difference (i.e., d-value), and mean. The calculations used in version 2.0.0 and onward differ from past calculations due to feedback during the journal review process. The new calculations allow for a more precise interpretation of the replication interval.
Author: David Stanley
Maintainer: David Stanley <dstanley@uoguelph.ca>

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Package GSODR updated to version 0.1.6 with previous version 0.1.5 dated 2016-05-16

Title: Download, Clean and Generate New Variables from GSOD Data
Description: Download, clean, reformat and create new variables from the USA National Climatic Data Center (NCDC) Global Surface Summary of the Day (GSOD) weather stations data, <https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod>. The function, get_GSOD(), retrieves data from the GSOD ftp site and reformats it from United States Customary System (USCS) units to International System of Units (SI), also for convenience elevation is converted from decimetres to metres. Stations are individually checked for number of missing days, as defined by the user, to assure data quality. Stations with too many missing observations are omitted from final file. Stations with missing latitude or longitude or values for both of 0 are omitted. Also omitted are stations with a latitude of < -90 or > 90 or longitude of < - 180 or > 180. Output is returned as a comma-separated values (CSV) file written to disk in a location selected by the user, which summarises each year by station and includes new variables: actual vapor pressure, saturation vapor pressure and relative humidity are calculated from the original GSOD data. The resulting files can be as large as 500mb depending on the user's stringency for missing data and geographic area of interest. Be sure to have sufficient RAM and disk space as well as a reasonably fast internet connection to use this package to perform this operation. However, for much smaller and more manageable data sets, an individual country of interest may be selected as well as only stations falling between -60/60 degrees latitude for agroclimatology work or individual stations if the station ID is known. The resulting files include station data (e.g., station name, country, latitude, longitude, elevation) for use in a geographic information system (GIS). The function was largely based on T. Hengl's 'getGSOD.R' script, available from <http://spatial-analyst.net/book/system/files/getGSOD.R> with enhancements to be more cross-platform, faster and more flexible. See the GSOD readme.txt <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre], Tomislav Hengl [ctb], Andy Nelson [ctb], Kay Sumfleth [ctb]
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package elliptic updated to version 1.3-7 with previous version 1.3-5 dated 2014-11-05

Title: Elliptic Functions
Description: A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between elliptic versions 1.3-5 dated 2014-11-05 and 1.3-7 dated 2016-05-26

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Package forecTheta updated to version 2.2 with previous version 2.1 dated 2016-03-07

Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models. Contains several cross-validation routines.
Author: Jose Augusto Fiorucci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>

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Package Davies updated to version 1.1-9 with previous version 1.1-8 dated 2012-11-07

Title: The Davies Quantile Function
Description: Various utilities for the Davies distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between Davies versions 1.1-8 dated 2012-11-07 and 1.1-9 dated 2016-05-26

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Package contfrac updated to version 1.1-10 with previous version 1.1-9 dated 2013-01-21

Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Wed, 25 May 2016

Package popprxl updated to version 0.1.2 with previous version 0.1.1 dated 2015-11-24

Title: Read GenAlEx Files Directly from Excel
Description: GenAlEx is a popular Excel macro for genetic analysis. The 'poppr' R package allows import of GenAlEx formatted CSV data. This package serves as a small 'poppr' add on for those who have trouble or simply do not want to export their data into CSV format.
Author: Zhian N. Kamvar [cre, aut], Niklaus J. Grünwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>

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Package openssl updated to version 0.9.4 with previous version 0.9.3 dated 2016-05-04

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut], Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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Package treescape updated to version 1.9.16 with previous version 1.8.16 dated 2016-04-01

Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treescapeServer()'.
Author: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>

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Package matlabr updated to version 1.1.3 with previous version 1.1 dated 2015-10-21

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

Diff between matlabr versions 1.1 dated 2015-10-21 and 1.1.3 dated 2016-05-25

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Package fslr updated to version 1.6.4.0 with previous version 1.5.0 dated 2015-10-21

Title: Wrapper Functions for FSL (FMRIB Software Library) from Functional MRI of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL (http:// fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used neuroimaging software, using system commands. The goal is to be able to interface with FSL completely in R, where you pass R objects of class "nifti", implemented by package 'oro.nifti', and the function executes an FSL command and returns an R object of class "nifti" if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package blackbox updated to version 1.0.8 with previous version 1.0 dated 2016-04-14

Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph], Leblois Raphaël [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between blackbox versions 1.0 dated 2016-04-14 and 1.0.8 dated 2016-05-25

 DESCRIPTION                  |   16 +++++-----
 MD5                          |   63 ++++++++++++++++++++++---------------------
 NAMESPACE                    |    2 -
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 34 files changed, 218 insertions(+), 187 deletions(-)

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Package Rlabkey updated to version 2.1.130 with previous version 2.1.129 dated 2015-12-15

Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

Diff between Rlabkey versions 2.1.129 dated 2015-12-15 and 2.1.130 dated 2016-05-25

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Package mlt.docreg updated to version 0.0-32 with previous version 0.0-30 dated 2016-02-24

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt.docreg versions 0.0-30 dated 2016-02-24 and 0.0-32 dated 2016-05-25

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Package mlt updated to version 0.0-33 with previous version 0.0-32 dated 2016-05-25

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt versions 0.0-32 dated 2016-05-25 and 0.0-33 dated 2016-05-25

 DESCRIPTION  |    8 ++++----
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Package mcPAFit updated to version 0.1.3 with previous version 0.1.2 dated 2016-05-17

Title: Estimating Preferential Attachment from a Single Network Snapshot by Markov Chain Monte Carlo
Description: A Markov chain Monte Carlo method is provided to estimate the preferential attachment function from a single network snapshot. Conventional methods require the complete information about the appearance order of all nodes and edges in the network. This package incorporates the appearance order into the state space and estimates it together with the preferential attachment function. Auxiliary variables are introduced to facilitate fast Gibbs sampling.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>

Diff between mcPAFit versions 0.1.2 dated 2016-05-17 and 0.1.3 dated 2016-05-25

 DESCRIPTION            |   14 
 MD5                    |   16 
 NAMESPACE              |    1 
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More information about mcPAFit at CRAN
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