CRAN (and crantastic) updates this week

New packages
------------

* bio3d (2.1-1)
  Maintainer: Barry Grant
  Author(s): Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
  License: GPL (>= 2)
  http://crantastic.org/packages/bio3d

  Utilities to process, organize and explore protein structure, 
  sequence and dynamics data.  Features include the ability to read
  and  write structure, sequence and dynamic trajectory data, perform
  sequence  and structure database searches, data summaries, atom
  selection,  alignment, superposition, rigid core identification,
  clustering,  torsion analysis, distance matrix analysis, structure
  and sequence  conservation analysis, normal mode analysis, principal
  component  analysis of heterogeneous structure data, and correlation
  network    analysis from normal mode and molecular dynamics data. 
  In addition,  various utility functions are provided to enable the
  statistical and  graphical power of the R environment to work with
  biological sequence  and structural data.  Please refer to the URLs
  below for more information.

* CLME (1.0-1)
  Maintainer: Casey M. Jelsema
  Author(s): Casey M. Jelsema
  License: GPL-2 | GPL-3
  http://crantastic.org/packages/CLME

  Implements constrained inference for linear mixed effects models using
  residual bootstrap methodology.

* CP (1.5)
  Maintainer: Andreas Kuehnapfel
  Author(s): Andreas Kuehnapfel
  License: GPL-3
  http://crantastic.org/packages/CP

  Functions for calculating the conditional power for different models
  in survival time analysis within randomized clinical trials with two
  different treatments to be compared and survival as an endpoint.

* dataRetrieval (1.4.0)
  Maintainer: Laura DeCicco
  Author(s): Robert Hirsch [aut], Laura DeCicco [aut, cre]
  License: Unlimited | file LICENSE
  http://crantastic.org/packages/dataRetrieval

  Collection of functions to help retrieve USGS data from either web
  services or user-provided data files.

* ecoval (1.0)
  Maintainer: Nele Schuwirth
  Author(s): Nele Schuwirth <nele.schuwi...@eawag.ch> and Peter Reichert
             <peter.reich...@eawag.ch>  with contributions by Simone
             Langhans
  License: GPL (>= 2)
  http://crantastic.org/packages/ecoval

  Functions for evaluating and visualizing ecological assessment
  procedures for surface waters containing physical, chemical and
  biological assessments in the form of value functions.

* enigma (0.1.0)
  Maintainer: Scott Chamberlain
  Author(s): Scott Chamberlain [aut, cre]
  License: MIT + file LICENSE
  http://crantastic.org/packages/enigma

  Enigma (https://enigma.io) holds many public datasets from
  governments, companies, universities, and organizations. Enigma
  provides an API for data, metadata, and statistics on each of the
  datasets. enigma is an R client to interact with the Enigma API,
  including getting the data and metadata for datasets in Enigma, as
  well as collecting statistics on datasets. In addition, you can
  download a gzipped csv file of a dataset if you want the whole
  dataset. An API key from Enigma is required to use enigma.

* flam (1.0)
  Maintainer: Ashley Petersen
  Author(s): Ashley Petersen
  License: GPL (>= 2)
  http://crantastic.org/packages/flam

  Implements the fused lasso additive model as proposed in Petersen, A.,
  Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv
  preprint arXiv:1409.5391.

* gets (0.1)
  Maintainer: Genaro Sucarrat
  Author(s): Genaro Sucarrat
  License: GPL-2
  http://crantastic.org/packages/gets

  Automated multi-path General-to-Specific (GETS) model selection of
  either an AR-X model with log-ARCH-X errors, or a log-ARCH-X model
  of the log-variance. The three main functions of the package are
  arx, getsm and getsv. The first function estimates an AR-X model
  with log-ARCH-X errors. The second function undertakes GETS model
  selection of the mean specification of an arx object, whereas the
  third function undertakes GETS model selection of the log-variance
  specification of an arx object.

* ggRandomForests (1.0.0)
  Maintainer: John Ehrlinger
  Author(s): John Ehrlinger <john.ehrlin...@gmail.com>
  License: GPL (>= 3)
  http://crantastic.org/packages/ggRandomForests

  The ggRandomForests package contains tools for creating and plotting
  data structures to visually understand random forest models. The
  functions are designed for use with the randomForestSRC package.
  This package is structured to extract intermediate data objects from
  the random forest. S3 Plot functions, which use the ggplot2 package,
  are included for each data object.

* highTtest (1.0)
  Maintainer: Shannon Holloway
  Author(s): Hongyuan Cao [aut], Michael Kosorok [aut], Shannon Holloway [aut, 
cre]
  License: GPL-2
  http://crantastic.org/packages/highTtest

  Implements the method developed by Cao and Kosorok (2011) for the
  significance analysis of thousands of features in high-dimensional
  biological studies. It is an asymptotically valid data-driven
  procedure to find critical values for rejection regions controlling
  the k-familywise error rate, false discovery rate, and the tail
  probability of false discovery proportion.

* landpred (1.0)
  Maintainer: Layla Parast
  Author(s): Layla Parast
  License: GPL
  http://crantastic.org/packages/landpred

  This package includes functions for landmark prediction of a survival
  outcome incorporating covariate and short-term event information.
  For more information about landmark prediction please see: Parast,
  Layla, Su-Chun Cheng, and Tianxi Cai. Incorporating short-term
  outcome information to predict long-term survival with discrete
  markers. Biometrical Journal 53.2 (2011): 294-307.

* logbin (1.0)
  Maintainer: Mark Donoghoe
  Author(s): Mark Donoghoe <mark.donog...@mq.edu.au>
  License: GPL (>= 2)
  http://crantastic.org/packages/logbin

  Methods for fitting log-link GLMs and GAMs for binomial data.  The
  package uses EM-type algorithms with more stable convergence
  properties than standard methods.

* logconPH (1.0)
  Maintainer: Clifford Anderson-Bergman
  Author(s): Clifford Anderson-Bergman
  License: GPL-2
  http://crantastic.org/packages/logconPH

  Computes a cox PH model with a log concave baseline distribution. If
  no covariates are provided, estimates the log concave NPMLE. Built
  specifically for interval censored data, where data is a n by 2
  matrix with [i, 1] as the left side of the interval for subject i
  and [i,2] as right side. Uncensored data can be entered by setting
  [i,1] = [i,2]. Alternatively, this can also handle uncensored data.
  If all the data is uncensored, you may enter data as a length(n)
  vector.

* mdscore (0.1-2)
  Maintainer: Antonio Hermes M. da Silva-Junior
  Author(s): Antonio Hermes M. da Silva-Junior [aut, cre], Damiao N. da Silva
             [aut], Silvia L. P. Ferrari [ctb]
  License: GPL (>= 2)
  http://crantastic.org/packages/mdscore

  A set of functions to obtain modified score test for generalized
  linear models.

* metaMix (0.1)
  Maintainer: Sofia Morfopoulou
  Author(s): Sofia Morfopoulou <sofia.morfopoulou...@ucl.ac.uk>
  License: GPL-3
  http://crantastic.org/packages/metaMix

  metaMix resolves complex metagenomic mixtures by analysing deep
  sequencing data, using a Mixture Model based approach. The use of
  parallel Monte Carlo Markov chains for the exploration of the
  species space enables the identification of the set of species more
  likely to contribute to the mixture.

* MRH (1.0)
  Maintainer: Yolanda Hagar
  Author(s): Yolanda Hagar, Yuanting Chen, Vanja Dukic
  License: GPL-2
  http://crantastic.org/packages/MRH

  Used on survival data to jointly estimate the hazard rate and the
  effects of covariates on failure times.

* nsgp (1.0.5)
  Maintainer: Markus Heinonen
  Author(s): Markus Heinonen
  License: GPL-2
  http://crantastic.org/packages/nsgp

  A Gaussian process regression using a Gaussian kernel for both
  one-sample and two-sample cases. Includes non-stationary Gaussian
  kernel (exponential decay function) and several likelihood ratio
  tests for differential testing along target points.

* pBrackets (1.0)
  Maintainer: ADES
  Author(s): Andreas Schulz
  License: GPL (>= 2.0)
  http://crantastic.org/packages/pBrackets

  Adds different kinds of brackets to a plot, including braces,
  chevrons, parentheses or square brackets.

* prettyunits (1.0.0)
  Maintainer: &quot;Gabor Csardi&quot;
  Author(s): "Gabor Csardi" [aut, cre]
  License: MIT + file LICENSE
  http://crantastic.org/packages/prettyunits

  Pretty, human readable formatting of quantities. Time intervals:
  1337000 -&gt; 15d 11h 23m 20s. Vague time intervals: 2674000 -&gt; about a
  month ago. Bytes: 1337 -&gt; 1.34 kB.

* QualInt (1.0.0)
  Maintainer: Lixi Yu
  Author(s): Lixi Yu, Eun-Young Suh, Guohua (James) Pan
  License: GPL-2
  http://crantastic.org/packages/QualInt

  Used for testing for qualitative interactions between treatment
  effects and patient subgroups. Here the term treatment effect means
  a comparison result of two treatments within each patient subgroup.
  Models included in this package are Gaussian, binomial and Cox
  models. Methods included here are interval based graphical approach
  and Gail Simon LRT.

* RCMIP5 (1.0)
  Maintainer: Kathe Todd-Brown
  Author(s): Ben Bond-Lamberty [aut], Kathe Todd-Brown [aut, cre]
  License: MIT + file LICENSE
  http://crantastic.org/packages/RCMIP5

  Working with CMIP5 data can be tricky, forcing scientists to write
  custom scripts and programs. The `RCMIP5` package aims to ease this
  process, providing a standard, robust, and high-performance set of
  scripts to (i) explore what data have been downloaded, (ii) identify
  missing data, (iii) average (or apply other mathematical operations)
  across experimental ensembles, (iv) produce both temporal and
  spatial statistical summaries, (v) regrid data, and (vi) produce
  easy-to-work-with graphical and data summaries.

* rex (0.1.0)
  Maintainer: Jim Hester
  Author(s): Kevin Ushey, Jim Hester
  License: MIT + file LICENSE
  http://crantastic.org/packages/rex

  A simpler, human-readable interface for the construction of regular
  expressions.

* rfoaas (0.0.4)
  Maintainer: Dirk Eddelbuettel
  Author(s): Dirk Eddelbuettel <e...@debian.org>
  License: GPL (>= 2)
  http://crantastic.org/packages/rfoaas

  R access to the FOAAS (F... Off As A Service) web service

* rivernet (1.0)
  Maintainer: Peter Reichert
  Author(s): Peter Reichert
  License: GPL (>= 2)
  http://crantastic.org/packages/rivernet

  Functions for reading, analysing and plotting river networks. For this
  package, river networks consist of sections and nodes with
  associated attributes,  e.g. to characterise their morphological,
  chemical and biological state. The package provides functions to
  read this data from text files, to analyse the network structure and
  network paths and regions consisting of sections and nodes that
  fulfill prescribed criteria, and to plot the river network and
  associated properties.

* RMKdiscrete (0.1)
  Maintainer: Robert M. Kirkpatrick
  Author(s): Robert M. Kirkpatrick <rkirkpatri...@vcu.edu>
  License: GPL (>= 2)
  http://crantastic.org/packages/RMKdiscrete

  Sundry discrete probability distributions and helper functions.

* segmag (1.2.2)
  Maintainer: Frank Papenmeier
  Author(s): Frank Papenmeier [aut, cre], Konstantin Sering [ctb]
  License: GPL (>= 3)
  http://crantastic.org/packages/segmag

  This package contains functions that help to determine event
  boundaries in event segmentation experiments by bootstrapping a
  critical segmentation magnitude under the null hypothesis that all
  key presses were randomly distributed across the experiment.
  Segmentation magnitude is defined as the sum of Gaussians centered
  at the times of the segmentation key presses performed by the
  participants. Within a participant, the maximum of the overlaid
  Gaussians is used to prevent an excessive influence of a single
  participant on the overall outcome (e.g. if a participant is
  pressing the key multiple times in succession). Further functions
  are included, such as plotting the results.

* sisVIVE (1.0)
  Maintainer: Hyunseung Kang
  Author(s): Hyunseung Kang <khy...@wharton.upenn.edu>
  License: GPL-2
  http://crantastic.org/packages/sisVIVE

  Selects invalid instruments amongst a candidate of potentially bad
  instruments. The algorithm selects potentially invalid instruments
  and provides an estimate of the causal effect between exposure and
  outcome. The paper, Instrumental Variables Estimation with Some
  Invalid Instruments and its Application to Mendelian Randomization
  by Hyunseung Kang, Anru Zhang, T. Tony Cai, and Dylan S. Small (on
  arXiv) has more details on this procedure.

* spark (1.0.0)
  Maintainer: &quot;Gabor Csardi&quot;
  Author(s): "Gabor Csardi" [aut, cre]
  License: MIT + file LICENSE
  http://crantastic.org/packages/spark

  Sparklines in the terminal. Essentially an R implementation of the
  original shell project: http://zachholman.com/spark/

* statar (0.1)
  Maintainer: Matthieu Gomez
  Author(s): Matthieu Gomez [aut, cre]
  License: GPL-2
  http://crantastic.org/packages/statar

  statar includes a set of functions for vectors: mode, tag, bin and
  winsorize. statar includes a set of functions for data.tables:
  summarize (in tables or graphs), panel data operations (lag, fill in
  gaps, fill in missing values) and SQL-type joins.

* vetools (1.3-28)
  Maintainer: Andrew Sajo-Castelli
  Author(s): Andrew Sajo-Castelli [aut, cre], Desiree Villalta [ctb], Lelys 
Bravo
             [ctb]
  License: GPL
  http://crantastic.org/packages/vetools

  Integrated data management library that offers a variety of tools
  concerning the loading and manipulation of environmental data
  available from different Venezuelan governmental sources. Facilities
  are provided to plot temporal and spatial data as well as understand
  the health of a collection of meteorological data.

* windex (1.0)
  Maintainer: Kevin Arbuckle
  Author(s): Kevin Arbuckle and Amanda Minter
  License: GPL-2
  http://crantastic.org/packages/windex

  Analysing convergent evolution using the Wheatsheaf index.


Updated packages
----------------

AICcmodavg (2.0-1), AlgDesign (1.1-7.3), ASMap (0.3-2), BcDiag
(1.0.5), circlize (0.1.2), clustvarsel (2.1), crayon (1.1.0), cwhmisc
(5.0), datamart (0.5.2), dice (1.2), eegkit (1.0-1), epinet (2.0.8),
evtree (1.0-0), frailtypack (2.7.2), GA (2.2), gsg (2.0), kselection
(0.1.1), matrixStats (0.10.3), mclogit (0.3-1), memisc (0.96-10), msBP
(1.0-1), MVN (3.5), NbClust (2.0.3), NPCirc (2.0.1), overlap (0.2.4),
pdc (1.0), PtProcess (3.3-7), R.devices (2.12.0), randomLCA (1.0-0),
raster (2.3-12), raster (2.3-10), rcdk (3.3.2), RcmdrPlugin.steepness
(0.3-2), rNOMADS (2.0.3), SCGLR (2.0.1), SemiParBIVProbit (3.2-12),
SMR (2.0), spgrass6 (0.8-6), spgwr (0.6-25), sptm (14.10-11), StMoSim
(3.0), stochvol (0.9-0), strvalidator (1.3.1), tis (1.27), utility
(1.3)



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