[R] CRAN (and crantastic) updates this week

Crantastic cranatic at gmail.com
Mon Sep 22 00:40:05 CEST 2014

CRAN (and crantastic) updates this week

New packages

* adaptDA (1.0)
  Maintainer: Charles Bouveyron
  Author(s): Charles Bouveyron
  License: GPL-2

  The adaptive mixture discriminant analysis (AMDA) allows to adapt a
  model-based classifier to the situation where a class represented in
  the test set may have not been encountered earlier in the learning

* aRxiv (0.5.2)
  Maintainer: Karl W Broman
  Author(s): Karthik Ram [aut], Karl Broman [aut, cre]
  License: MIT + file LICENSE

  An interface to the API for arXiv, a repository of electronic
  preprints for computer science, mathematics, physics, quantitative
  biology, quantitative finance, and statistics.

* audited (1.9)
  Maintainer: Tim Bergsma
  Author(s): Tim Bergsma
  License: GPL

  Classifies a data.frame such that row deletions and additions are
  tracked.  A mechanism exists to give formal names to the row subsets
  that are coming or going.  These names are used to populate a
  directed graph giving an account of all the transactions
  contributing to the state of the data.frame.  The generic
  as.audited() has a method for keyed data.frames that creates an
  audited data.frame. Methods exist that track row count changes for
  the generics: Ops, !, ^, |, [, subset, head, tail, unique, cast,
  melt, aggregate, and merge. audit() extracts the transaction table
  from the audited object, while write.audit() and read.audit()
  control exchange with the file system. An audit method for
  as.igraph() creates a graph object that can be displayed with the
  corresponding plot method.  Use options(audit= )  to provide an
  extra level of classification. Use options(artifact=TRUE)  and
  as.xlsx() to save dropped records to file.

* BEANSP (1.0)
  Maintainer: Yiqun Yang
  Author(s): Chong He, Yiqun Yang, Jing Cao
  License: GPL-2

  Computing age specific nest survival rates based on a Bayesian
  hierarchical model. This package can handle unknown nest age,
  irregular visiting schedule and nest-specific covariates.

* binequality (0.6.1)
  Maintainer: Samuel V. Scarpino
  Author(s): Samuel V. Scarpino, Paul von Hippel, and Igor Holas
  License: GPL (>= 3.0)

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

* BOIN (1.0)
  Maintainer: Ying Yuan
  Author(s): Ying Yuan and Suyu Liu
  License: GPL-2

  The Bayesian optimal interval (BOIN) design is a novel phase I
  clinical trial design for finding the maximum tolerated dose (MTD).
  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 average performance comparable to the continual reassessment
  method (CRM, one of the best model-based design) in terms of
  selecting the MTD, but has a substantially lower risk of assigning
  patients to subtherapeutic or overly toxic doses.

* confidence (1.0-0)
  Maintainer: Dennis Walvoort
  Author(s): Willem M. G. M. van Loon [aut, cph], Dennis J. J. Walvoort [aut, cre]
  License: GPL (>= 3)

  Functions for estimating and reporting multiyear averages and
  corresponding confidence intervals and distributions. A potential
  use case is reporting the chemical and ecological status of surface
  waters according to the European Water Framework Directive.

* GlobalOptions (0.0.1)
  Maintainer: Zuguang Gu
  Author(s): Zuguang Gu
  License: GPL (>= 2)

  Generate functions to get or set global options

* hot.deck (1.0)
  Maintainer: Dave Armstrong
  Author(s): Skyler Cranmer, Jeff Gill, Natalie Jackson, Andreas Murr, Dave
  License: GPL (>= 2)

  Performs multiple hot-deck imputation of categorical and continuous
  variables in a data frame.

* iki.dataclim (1.0)
  Maintainer: Boris Orlowsky
  Author(s): Boris Orlowsky
  License: GPL-3

  The package offers an S4 infrastructure to store climatological
  station data of various temporal aggregation scales. In-built
  quality control and homogeneity tests follow the methodology from
  the European Climate Assessment & Dataset project. Wrappers for
  climate indices defined by the Expert Team on Climate Change
  Detection and Indices (ETCCDI), a quick summary of important climate
  statistics and climate diagram plots provide a fast overview of
  climatological characteristics of the station.

* kselection (0.1.0)
  Maintainer: Daniel Rodriguez Perez
  Author(s): Daniel Rodriguez Perez
  License: GPL-3

  Selection of k in k-means clustering based on Pham et al. paper
  ``Selection of k in k-means clustering''

* m4fe (0.1)
  Maintainer: Nathan Esau
  Author(s): Nathan Esau <nesau at sfu.ca>
  License: GPL-2

  Provides binomial tree models for European, American and Asian Options
  as well as Interest Rates. Monte Carlo Simulation and Methods for
  Solving Differential Equations are also included.

* MatchingFrontier (0.3.17)
  Maintainer: Christopher Lucas
  Author(s): Gary King, Christopher Lucas, and Richard Nielsen
  License: GPL-3

  MatchingFrontier returns the subset of the data with the minimum
  imbalance for  	     every possible subset size (N - 1, N - 2, ...),
  down to the data set with the  	     minimum possible imbalance. The
  package also includes tools for the estimation 	     of causal
  effects for each subset size, as well as functions for visualization
  and data export.

* MST (1.0)
  Maintainer: Peter Calhoun
  Author(s): Xiaogang Su, Peter Calhoun, and Juanjuan Fan
  License: GPL-2

  Constructs trees for multivariate survival data using marginal and
  frailty models

* multipleNCC (1.0)
  Maintainer: Nathalie C. Stoer
  Author(s): Nathalie C. Stoer, Sven Ove Samuelsen
  License: GPL-2

  This package fit Cox proportional hazard models with a weighted 
  partial likelihood. It handles one or multiple endpoints, additional
  matching  and makes it possible to reuse controls for other

* nat.nblast (1.5)
  Maintainer: James Manton
  Author(s): Greg Jefferis and James Manton
  License: GPL-3

  Extends package nat (NeuroAnatomy Toolbox) by providing a collection
  of NBLAST-related functions.

* nat.templatebrains (0.4.1)
  Maintainer: James Manton
  Author(s): James Manton and Greg Jefferis
  License: GPL-3

  Extends package nat (NeuroAnatomy Toolbox) by providing objects and
  functions for handling template brains.

* nlWaldTest (1.0.1)
  Maintainer: Oleh Komashko
  Author(s): Oleh Komashko
  License: GPL (>= 2)

  Nonlinear restrictions Wald Test for regression parameters using

* opentraj (1.0)
  Maintainer: Thalles Silva
  Author(s): Thalles Santos Silva
  License: GPL-2

  opentraj uses the Hybrid Single Particle Lagrangian Integrated
  Trajectory Model (HYSPLIT) for computing simple air parcel
  trajectories. The functions in this package allow users to run
  HYSPLIT for trajectory calculations, as well as get its results,
  directly from R without using any GUI interface.

* polidata (0.1.0)
  Maintainer: Eunjeong Park
  Author(s): Eunjeong Park [aut, cre], Jong Hee Park [aut]
  License: MIT + file LICENSE

  This package provides easy access to various political data APIs
  directly from R. For example, you can access Google Civic
  Information API (https://developers.google.com/civic-information/)
  or Sunlight Congress API (https://sunlightlabs.github.io/congress/)
  for US Congress data, and POPONG API (http://data.popong.com/) for
  South Korea National Assembly data.

* powerr (0.1-3)
  Maintainer: Jingfan Sun
  Author(s): Jingfan Sun [aut, cre]
  License: GPL (>= 2)

  'powerr' is used for electric power system analysis and control,
  including basic power flow analysis and CASCADE analysis. Other
  features will be updated soon.

* propOverlap (1.0)
  Maintainer: Osama Mahmoud
  Author(s): Osama Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad
             Khan, Berthold Lausen
  License: GPL (>= 2)

  A package for selecting the most relevant features (genes) in the
  high-dimensional binary classification problems. The discriminative
  features are identified using analyzing the overlap between the
  expression values across both classes. The package includes
  functions for measuring the proportional overlapping score for each
  gene avoiding the outliers effect. The used measure for the overlap
  is the one defined in the "Proportional Overlapping Score (POS)"
  technique for feature selection. A gene mask which represents a
  gene's classification power can also be produced for each gene
  (feature). The set size of the selected genes might be set by the
  user. The minimum set of genes that correctly classify the maximum
  number of the given tissue samples (observations) can be also

* qdapRegex (0.1.1)
  Maintainer: Tyler Rinker
  Author(s): Jason Gray [ctb], Tyler Rinker [aut, cre]
  License: GPL-2

  A collection of regex tools associated with the qdap package that may
  be useful outside of the context of discourse analysis.  Tools
  include removal/extraction/replacement of abbreviations, dates,
  dollar amounts, email addresses, hash tags, numbers, percentages,
  person tags, phone numbers, times, and zip codes.

* qgtools (1.0)
  Maintainer: Jixiang Wu
  Author(s): Jixiang Wu (South Dakota State University), Johnie N. Jenkins and Jack
             C. McCarty (USDA-ARS)
  License: GPL-2

  Two linear mixed model approaches: REML(restricted maximum likelihood)
  and MINQUE (minimum norm quadratic unbiased estimation) approaches
  and several resampling techniques are integrated for various
  quantitative genetics analyses. With these two types of approaches,
  various unbalanced data structures, missing data, and any irregular
  genetic  mating designs can be analyzed and statistically tested.
  This package also offers fast computations for many large data sets.
  Other functions will be added to this R tool in the future.

* redcapAPI (1.0)
  Maintainer: Benjamin Nutter
  Author(s): Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with
             contributions from Jeremy Stephens, and Will Beasley
  License: GPL-2

  Access data stored in REDCap databases using the Application
  Programming Interface (API).  REDCap (Research Electronic Data
  CAPture) is a web application for building and managing online
  surveys and databases developed at Vanderbilt University.  The API
  allows users to access data and project meta data (such as the data
  dictionary) from the web programmatically.  The redcapAPI package
  facilitates the process of accessing data with options to prepare an
  analysis-ready data set consistent with the definitions in a
  database's data dictionary.

* REDCapR (0.4-28)
  Maintainer: Will Beasley
  Author(s): Will Beasley [aut, cre], David Bard [ctb], Thomas Wilson [ctb], John J
             Aponte [ctb], Rollie Parrish [ctb]
  License: GPL-3

  Encapsulates functions to streamline calls from R

* rmarkdown (0.3.3)
  Maintainer: JJ Allaire
  Author(s): JJ Allaire, Jonathan McPherson, Yihui Xie, Hadley Wickham, Joe Cheng,
             Jeff Allen
  License: GPL-3

  Convert R Markdown documents into a variety of formats including HTML,
  MS Word, PDF, and Beamer.

* RMOA (1.0)
  Maintainer: Jan Wijffels
  Author(s): Jan Wijffels [aut, cre], BNOSAC [cph]
  License: GPL-3

  Connect R with MOA (Massive Online Analysis -
  http://moa.cms.waikato.ac.nz) to build classification models and
  regression models on streaming data or out-of-RAM data

* RMOAjars (1.0)
  Maintainer: Jan Wijffels
  Author(s): See file AUTHORS
  License: GPL-3

  External jars required for package RMOA. RMOA is a framework to build
  data stream models on top of MOA (Massive Online Analysis -

* RRreg (0.1.3)
  Maintainer: Daniel W. Heck
  Author(s): Daniel W. Heck [aut, cre], Morten Moshagen [aut]
  License: GPL-2

  RRreg provides univariate and multivariate methods to analyze
  randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
  Randomized response: A survey technique for eliminating evasive
  answer bias. Journal of the American Statistical Association, 60,
  63–69). Besides univariate estimates of true proportions, RR
  variables can be used for correlations, as dependent variable in a
  logistic regression and as predictors in a linear regression. For
  simulation and bootstrap purposes, RR data can be generated
  according to several models.

* smoother (
  Maintainer: Nicholas Hamilton
  Author(s): Nicholas Hamilton
  License: GPL-2

  A port of the matlab gaussian window smoothing function

* SOR (0.22)
  Maintainer: Lee S. McDaniel
  Author(s): Lee S. McDaniel, Jonathan S. Schildcrout
  License: GPL (>= 2)

  Estimation for longitudinal data following outcome dependent sampling
  using the sequential offsetted regression technique.  Includes
  support for binary, count, and continuous data.

* spatialnbda (1.0)
  Maintainer: Glenna Nightingale
  Author(s): Glenna Nightingale
  License: GPL

  Network based diffusion analysis (NBDA) allows inference on the
  asocial and social transmission of information.  This may involve
  the social transmission of a particular behaviour such as tool use,
  for example. For the NBDA, the key parameters estimated are the
  social effect and baseline rate  parameters.  The baseline rate
  parameter gives the rate at which the behaviour is first performed
  (or acquired) asocially amongst the individuals in a given
  population. The social effect parameter quantifies the effect of the
  social associations amongst  the individuals on the rate at which
  each individual first performs or displays the behaviour.  Spatial
  NBDA involves incorporating spatial information in the analysis.  
  This is done by incorporating social networks derived from  spatial
  point patterns (of the home bases of the individuals under study). 
  In addition,  a spatial covariate such as vegetation cover, or slope
  may be included in the modelling process.

* UPMASK (1.0)
  Maintainer: Alberto Krone-Martins
  Author(s): Alberto Krone-Martins, Andre Moitinho
  License: GPL (>= 3)

  An implementation of the UPMASK method for performing membership
  assignment in stellar clusters in R. It is prepared to use
  photometry and spatial positions, but it can take into account other
  types of data. The method is able to take into account arbitrary
  error models, and it is unsupervised, data-driven,
  physical-model-free and relies on as few assumptions as possible.
  The approach followed for membership assessment is based on an
  iterative process, principal component analysis, a clustering
  algorithm and a kernel density estimation.

* uskewFactors (1.0)
  Maintainer: Paula M. Murray
  Author(s): Paula M. Murray, Ryan P. Browne, and Paul D. McNicholas
  License: GPL (>= 2)

  Implements mixtures of unrestricted skew-t factor analyzer models via
  the EM algorithm

* vdmR (0.1.0)
  Maintainer: Tomokazu Fujino
  Author(s): Tomokazu Fujino
  License: GPL-2

  This provides web based visual data mining tools by adding interactive
  functions to ggplot2 graphics. Brushing and linking between the
  multiple plots is one of the main feature of this package. Currently
  scatter plot, histogram, parallel coordinate plot and choropleth map
  are supported.

Updated packages

allelematch (2.5), bbo (0.2), beanplot (1.2), betategarch (3.2),
bReeze (0.4-0), coin (1.0-24), compute.es (0.2-4), corHMM (1.15),
demography (1.18), DirichletReg (0.5-2), DirichletReg (0.5-1),
Distance (0.9.2), dlm (1.1-4), dsm (2.2.5), fCopulae (3011.81), fmsb
(0.5.1), fRegression (3011.81), gamlr (1.12), gamlss (4.3-1),
gamlss.dist (4.3-1), gdsfmt (, genlasso (1.3), geostatsp
(1.0.0), geostatsp (1.0.1), gplots (2.14.2), GuardianR (0.5),
intervals (0.15.0), investr (1.1.2), ivbma (1.05), LiblineaR
(1.80-10), llama (0.7.2), LogicForest (2.1.0), mclust (4.4), mco
(1.0.13), mitools (2.3), modTempEff (1.5.2), mrds (2.1.8), ncdf4
(1.13), nontarget (1.5), OrdLogReg (1.1), party (1.0-17), pcaPP
(1.9-50), PerformanceAnalytics (1.4.3541), PivotalR (,
protViz (0.2.06), qat (0.73), qpcR (1.4-0), RadioSonde (1.4),
RcppOctave (0.14.5), refGenome (1.3.0), repmis (0.3), rgdal (0.9-1),
rms (4.2-1), rredis (1.6.9), RUnit (0.4.27), RVAideMemoire (0.9-39),
shapes (1.1-10), SmoothHazard (1.2.0), SmoothHazard (1.2.3), spdep
(0.5-77), spMC (0.3.4), SSDforR (1.4.7), Taxonstand (1.4), TreeSim

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