[R] CRAN (and crantastic) updates this week

Crantastic cranatic at gmail.com
Mon Nov 10 00:40:05 CET 2014

CRAN (and crantastic) updates this week

New packages

* anim.plots (0.1)
  Maintainer: David Hugh-Jones
  Author(s): David Hugh-Jones <davidhughjones at gmail.com>
  License: GPL-2

  Simple animated versions of basic R plots, using the 'animation'
  package. Includes animated versions of plot, barplot, persp,
  contour, filled.contour, hist, curve, points, lines, text, symbols,
  segments, and arrows.

* aoos (0.0.1)
  Maintainer: Sebastian Warnholz
  Author(s): Sebastian Warnholz
  License: GPL-3 | file LICENSE

  Another implementation of object-orientation in R. Private and public
  methods are part of the class-definition. Allows to write a lot of
  small methods as part of the class definition without cluttering the

* CpGFilter (1.0)
  Maintainer: Jun Chen
  Author(s): Jun Chen
  License: GPL-2

  Filter CpGs based on Intra-class Correlation Coefficients (ICCs) when
  replicates are available. ICCs are calculated by fitting linear
  mixed effects models to all samples including the un-replicated
  samples. Including the large number of un-replicated samples
  improves ICC estimates dramatically. The method accommodates any
  replicate design.

* dfcomb (1.0-1)
  Maintainer: Marie-Karelle Riviere
  Author(s): Marie-Karelle Riviere and Jacques-Henri Jourdan
  License: GPL-3

  Phase I/II adaptive dose-finding design for combination studies.
  Several methods are proposed depending on the type of combinations:
  (1) the combination of two cytotoxic agents, and (2) combination of
  a molecularly targeted agent with a cytotoxic agent.

* dfmta (1.0-1)
  Maintainer: Marie-Karelle Riviere
  Author(s): Marie-Karelle Riviere and Jacques-Henri Jourdan
  License: GPL-3

  Phase I/II adaptive dose-finding design for single-agent Molecularly
  Targeted Agent (MTA), according to the paper "Phase I/II
  Dose-Finding Design for Molecularly Targeted Agent: Plateau
  Determination using Adaptive Randomization", Statistics in Medicine,

* dummy (0.1.0)
  Maintainer: Michel Ballings
  Author(s): Michel Ballings and Dirk Van den Poel
  License: GPL (>= 2)

  Efficiently create dummies of all factors and character vectors in a
  data frame. Support is included for learning the categories on one
  data set (e.g., a training set) and deploying them on another (e.g.,
  a test set).

* FAMILY (0.1.18)
  Maintainer: Asad Haris
  Author(s): Asad Haris
  License: GPL (>= 2)

  Fits penalized linear and logistic regression models with pairwise
  interaction terms.

* geesmv (1.0)
  Maintainer: Zheng Li
  Author(s): Ming Wang <mwang at phs.psu.edu>
  License: GPL (>= 3)

  Generalized estimating equations with the original sandwich variance
  estimator proposed by Liang and Zeger (1986), and eight types of
  more recent modified variance estimators for improving the finite
  small-sample performance.

* geocodeHERE (0.1)
  Maintainer: Cory Nissen
  Author(s): "Cory Nissen <corynissen at gmail.com> [aut, cre]"
  License: MIT + file LICENSE

  Wrapper for Nokia's HERE geocoding API. See http://here.com/ for more
  information on HERE and https://developer.here.com/geocoder for more
  information on the HERE geocoding API.

* ggswissmaps (0.0.2)
  Maintainer: Sandro Petrillo Burri
  Author(s): Sandro Petrillo Burri <gibo.gaf at gmail.com>
  License: GPL-2

  Offers various swiss maps as ggplot2 objects and gives the possibility
  to add layers of data on the maps. Data are publicly available from
  the swiss federal statistical office.

* hcp (0.1)
  Maintainer: Yulei Wang
  Author(s): Stephen J.Ganocy, Jiayang Sun, and Yulei Wang
  License: GPL-2 | GPL-3

  Estimation of parameters in 3-segment (i.e. 2 change-point) regression
  models with heteroscedastic variances is provided based on both
  likelihood and hybrid Bayesian approaches, with and without
  continuity constraints at the change points.

* heritability (1.0)
  Maintainer: Willem Kruijer
  Author(s): Willem Kruijer, with a contribution from Ian White (the internal
             function pin). Contains data collected by Padraic Flood
             and Rik Kooke.
  License: GPL-3

  implements marker-based estimation of heritability when observations
  on genetically identical replicates are available. These can be
  either observations on individual plants or plot-level data in a
  field trial. Heritability can then be estimated using a mixed model
  for the individual plant or plot data. For comparison, also
  mixed-model based estimation using genotypic means and estimation of
  repeatability with ANOVA are implemented. For illustration the
  package contains several datasets for the model species Arabidopsis

* ionflows (1.0)
  Maintainer: Michael Bockmayr
  Author(s): Michael Bockmayr and Jan Budczies
  License: GPL-3

  Two methods for calculation of the number of required flows for
  semiconductor sequencing: 1. Using a simulation, the number of flows
  can be calculated for a concrete list of amplicons. 2. An exact
  combinatorial model is evaluated to calculate the number of flows
  for a random ensemble of sequences.

* LinCal (1.0)
  Maintainer: Derick L. Rivers
  Author(s): Derick L. Rivers <riversdl at vcu.edu> and Edward L. Boone
  License: GPL-2

  Estimate and confidence/credible intervals for an unknown regressor x0
  given an observed y0.

* lpme (1.0.0)
  Maintainer: Haiming Zhou
  Author(s): Haiming Zhou <zhouh at email.sc.edu> and Xianzheng Huang
             <huang at stat.sc.edu>
  License: GPL (>= 2)

  Two local polynomial estimators for solving the errors-in-variables
  problem: one is in Delaigle, Fan, and Carroll (2009), and one is in
  Huang and Zhou (2014+). The SIMEX bandwidth selection method is also
  provided for both estimators.

* MGL (1.1)
  Maintainer: Safiye Celik
  Author(s): Safiye Celik
  License: GPL (>= 2)

  An aggressive dimensionality reduction and network estimation
  technique for a high-dimensional Gaussian graphical model (GGM).
  Please refer to: Efficient Dimensionality Reduction for
  High-Dimensional Network Estimation, Safiye Celik, Benjamin A.
  Logsdon, Su-In Lee, Proceedings of The 31st International Conference
  on Machine Learning, 2014, p. 1953--1961.

* OptionPricing (0.1)
  Maintainer: Wolfgang Hormann
  Author(s): Kemal Dingec, Wolfgang Hormann
  License: GPL-2 | GPL-3

  Efficient Monte Carlo Algorithms for the price and the sensitivities
  of Asian and European Options under Geometric Brownian Motion.

* PANDA (0.9.9)
  Maintainer: Hua Li
  Author(s): Hua Li and Pan Tong
  License: Artistic-2.0

  PANDA (Preferential Attachment based common Neighbor Distribution
  derived Associations) is designed to perform the following tasks in
  PPI networks: (1) identify significantly functionally associated
  protein pairs, (2) predict GO terms and KEGG pathways for proteins,
  (3) make a cluster of proteins based on the significant protein
  pairs, (4) identify subclusters whose members are enriched in KEGG
  pathways. For other types of biological networks, (1) and (3) can
  still be performed.

* pez (0.9-0)
  Maintainer: William D. Pearse
  Author(s): William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares, Caroline
             Tucker, Steve C. Walker, Matthew R. Helmus
  License: GPL-3

  Eco-phylogenetic and community phylogenetic analyses. Keeps community
  ecological and phylogenetic data matched up and comparable using
  'comparative.comm' objects. Wrappers for common community
  phylogenetic indices ('shape', 'evenness', 'dispersion', and
  'dissimilarity' metrics). Implementation of Cavender-Bares (2004)
  correlation of phylogenetic and ecological matrices
  ('fingerprint.regression'). Simulation of null assemblages, traits,
  and phylogenies ('scape', 'sim.meta.comm').

* PLSbiplot1 (0.1)
  Maintainer: Opeoluwa F. Oyedele
  Author(s): Opeoluwa F. Oyedele [aut, cre], Sugnet Gardner-Lubbe [aut]
  License: GPL-2

  Principal Component Analysis (PCA) biplots, Covariance monoplots and
  biplots, Partial Least Squares (PLS) biplots, Partial Least Squares
  for Generalized Linear Model (PLS-GLM) biplots, Sparse Partial Least
  Squares (SPLS) biplots and Sparse Partial Least Squares for
  Generalized Linear Model (SPLS-GLM) biplots.

* poplite (0.99.5)
  Maintainer: Daniel Bottomly
  Author(s): Daniel Bottomly
  License: GPL-3

  Provides objects and accompanying methods which facilitates populating
  and querying SQLite databases.

* prc (2014.11-4)
  Maintainer: Youyi Fong
  Author(s): Youyi Fong
  License: GPL (>= 2)

  Estimation, prediction and testing for analyzing serial dilution assay
  data using paired response curve.

* ScoreGGUM (1.0)
  Maintainer: David R. King
  Author(s): David R. King and James S. Roberts
  License: GPL (>= 2)

  Estimate GGUM Person Parameters Using Pre-Calibrated Item Parameters
  and Binary or Graded Disagree-Agree Responses

* sdcTarget (0.9-11)
  Maintainer: Emmanuel Lazaridis
  Author(s): Emmanuel Lazaridis [aut, cre]
  License: CC BY-NC 4.0

  Classes and methods to calculate and evaluate target matrices for
  statistical disclosure control.

* snht (1.0)
  Maintainer: Josh Browning
  Author(s): Josh Browning
  License: GPL-3

  Robust and non-robust SNHT tests for changepoint detection.

* spareserver (1.0.0)
  Maintainer: "Gabor Csardi"
  Author(s): "Gabor Csardi" [aut, cre]
  License: MIT + file LICENSE

  Client size load balancing. Decide which server to connect to, based
  on previous response times, and configuration.

* sudokuAlt (0.1-2)
  Maintainer: Bill Venables
  Author(s): Bill Venables <Bill.Venables at gmail.com>
  License: GPL (>= 2)

  Tools for making, retrieving, displaying and solving sudoku games.
  This package is an alternative to the earlier sudoku-solver package,
  'sudoku'.  The present package uses a slightly different algorithm,
  has a simpler coding and presents a few more sugar tools, such as
  plot and print methods.

* TRSbook (1.0.1)
  Maintainer: P. Lafaye de Micheaux
  Author(s): Lafaye de Micheaux Pierre, Drouilhet Remy, Liquet Benoit
  License: GPL (>= 2)

  Functions and datasets for the reader of the book "The R Software:
  Fundamentals of Programming and Statistical Analysis".

* Watersheds (1.0)
  Maintainer: J. A. Torres
  Author(s): J.A. Torres
  License: GPL (>= 2)

  Methods for watersheds aggregation and spatial drainage network

* WhiteStripe (1.0)
  Maintainer: John Muschelli
  Author(s): Taki Shinohara, John Muschelli
  License: GPL-2

  Whitestripe normalization from Shinohara et. al does For
  intensity-based normalization of T1 and T2 images, where normal
  appearing white matter performs well, but requires segmentation. 
  This method performs white matter mean and standard deviation
  estimates on data that has been rigidly-registered to the MNI
  template and uses histogram-based methods.

* wikipediatrend (0.2.0)
  Maintainer: Peter Meissner
  Author(s): Peter Meissner [aut, cre], R Core team [ctb] (wp_date derived from
             base package as.Date)
  License: GPL (>= 2)

  Public attention is an interesting field of study. The internet not
  only allows to access information in no time on virtually any
  subject but via page access statistics gathered by website authors
  the subject of attention as well can be studied. For the omnipresent
  Wikipedia those access statistics are made available via
  stats.grok.se a server providing the information as file dumps as
  well as as web API. This package provides an easy to  use,
  consistent and traffic minimizing approach to make those data
  accessible within R.

* xtal (1.0)
  Maintainer: Qingan Sun
  Author(s): Qingan Sun, Xiaojun Li
  License: GPL-2 | GPL-3

  Tool set for crystallographer to design and analyze crystallization
  experiments of ribosome from Mycobacterium tuberculosis

Updated packages

afex (0.12-135), aRxiv (0.5.5), bayesTFR (4.0-9), BayesTree (0.3-1.2),
BB (2014.10-1), biwavelet (0.17.5), biwavelet (0.17.4), BNSP (1.0.1),
BTYD (2.4), circlize (0.1.3), cvAUC (1.0.1), descr (1.0.4), dfcomb
(1.0-1), dfmta (1.0-1), dglm (1.8), dglm (1.8.1), diagram (1.6.3), dma
(1.2-2), elliptic (1.3-5), extraTrees (1.0.4), feature (1.2.11), FME
(1.3.2), gdimap (0.1-8), geometry (0.3-5), geomorph (2.1.2), GGIR
(1.1-4), hypergeo (1.2-9), limSolve (, lpSolveAPI
(, marelac (2.1.4), marmap (0.9), MAT (2.2), MGL (1.1),
msgl (, NMOF (0.34-0), openssl (0.2), ordinalgmifs (1.0.2),
pca3d (0.3), pracma (1.7.7), prim (1.0.15), pvar (2.0), Quandl
(2.4.0), readBrukerFlexData (1.8.1), Rfit (0.21), rgbif (0.7.7),
RJSDMX (1.2), rminer (1.4), RobustAFT (1.3), rootSolve (,
RPPanalyzer (1.4), rugarch (1.3-4), shape (1.4.2), SKAT (1.0.1),
snpEnrichment (1.6.0), sqldf (0.4-10), SSN (1.1.4), tagcloud (0.5),
tagcloud (0.4), tm.plugin.webmining (1.2.2), TreePar (3.2), trip
(1.1-19), TRSbook (1.0.1), usl (1.4.0), vcrpart (0.2-2), VGAM (0.9-5),
VGAMdata (0.9-5), WARN (1.1), weightedScores (0.9.1)

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