[R] CRAN (and crantastic) updates this week

Crantastic cranatic at gmail.com
Mon Sep 15 00:40:06 CEST 2014

CRAN (and crantastic) updates this week

New packages

* cmvnorm (1.0)
  Maintainer: Robin Hankin
  Author(s): Robin K. S. Hankin
  License: GPL-2

  various utilities for the complex multivariate Gaussian distribution

* couchDB (1.3.0)
  Maintainer: Aleksander Dietrichson
  Author(s): Aleksander Dietrichson
  License: AGPL-3

  Interface to couchDB

* eegkit (1.0-0)
  Maintainer: Nathaniel E. Helwig
  Author(s): Nathaniel E. Helwig <helwig at umn.edu>
  License: GPL (>= 2)

  Analysis and visualization tools for electroencephalography (EEG)
  data. Includes functions for plotting (a) EEG caps, (b) single- and
  multi-channel EEG time courses, and (c) EEG spatial maps. Also
  includes smoothing and Independent Component Analysis functions for
  EEG data analysis.

* eegkitdata (1.0)
  Maintainer: Nathaniel E. Helwig
  Author(s): Nathaniel E. Helwig <helwig at umn.edu>
  License: GPL (>= 2)

  Contains the example EEG data used in the package eegkit. Also
  contains code for easily creating larger EEG datasets from the EEG
  Database on the UCI Machine Learning Repository.

* ForwardSearch (1.0)
  Maintainer: Bent Nielsen
  Author(s): Bent Nielsen
  License: GPL-3

  Forward Search analysis of time series regressions. Implements the
  asymptotic theory developed in Johansen and Nielsen (2013, 2014).

* FRESA.CAD (1.0)
  Maintainer: Jose Gerardo Tamez-Pena
  Author(s): Jose Gerardo Tamez-Pena
  License: LGPL (>= 2)

  FRESA.CAD provides a set of functions and feature selection algorithms
  for building Computer Aided Diagnosis Models

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

  The funFEM algorithm (Bouveyron et al., 2014) allows to cluster
  functional data by modeling the curves within a common and
  discriminative functional subspace.

* funHDDC (1.0)
  Maintainer: Charles Bouveyron
  Author(s): C. Bouveyron & J. Jacques
  License: GPL-2

  The package provides the funHDDC algorithm (Bouveyron & Jacques, 2011)
  which allows to cluster functional data by modeling each group
  within a specific functional subspace.

* gapmap (0.0.1)
  Maintainer: Ryo Sakai
  Author(s): Ryo Sakai
  License: GPL-2 | GPL-3

  The gap encodes the distance between clusters and improves
  interpretation of cluster heatmaps. The gaps can be of the same
  distance based on a height threshold to cut the dendrogram. Another
  option is to vary the size of gaps based on the distance between

* GENLIB (1.0)
  Maintainer: Marie-Helene Roy-Gagnon
  Author(s): Louis Houde, Jean-Francois Lefebvre, Valery Roy-Lagace, Sebastien
  License: GPL (>= 2)

  Takes genealogical data frames and calculates different demographic
  variables such as genetic contribution, kinship, etc...

* lefse (0.1)
  Maintainer: Nathan G. Swenson
  Author(s): Nathan G. Swenson
  License: GPL-2 | GPL-3

  Utilizing phylogenetic and functional information for the analyses of
  ecological datasets. The analyses include methods for quantifying
  the phylogenetic and functional diversity of assemblages.

* lunar (0.1-04)
  Maintainer: Emmanuel Lazaridis
  Author(s): Emmanuel Lazaridis [aut, cre]
  License: MIT + file LICENSE

  Provides functions to calculate lunar and other environmental

* micropan (1.0)
  Maintainer: Lars Snipen
  Author(s): Lars Snipen and Kristian Hovde Liland
  License: GPL-2

  A collection of functions for computations and visualizations of
  microbial pan-genomes.

* nettools (1.0.1)
  Maintainer: Michele Filosi
  Author(s): Michele Filosi [aut, cre], Roberto Visintainer [aut], Samantha
             Riccadonna [aut], Giuseppe Jurman [ctb], Cesare
             Furlanello [ctb]
  License: CC BY-NC-SA 4.0

  A collection of network inference methods for co-expression networks,
  quantitative network distances and a novel framework for network
  stability analysis.

* RDML (0.4-2)
  Maintainer: Konstantin A. Blagodatskikh
  Author(s): Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal
             Burdukiewicz [aut]
  License: GPL (>= 2)

  Imports real-time thermo cycler (qPCR) data from RDML format files and
  transforms to the appropriate formats of the 'qpcR' and 'chipPCR'

* saery (1.0)
  Maintainer: Agustin Perez Martin
  Author(s): Maria Dolores Esteban Lefler, Domingo Morales Gonzalez, Agustin Perez
  License: GPL-2

  A complete set of functions to calculate several EBLUP (Empirical Best
  Linear Unbiased Predictor) estimators and their mean squared errors.
  All estimators are based on an area-level linear mixed model
  introduced by Rao and Yu in 1994 (see documentation). The REML
  method is used for fitting this model.

* slackr (1.2)
  Maintainer: Bob Rudis
  Author(s): Bob Rudis (@hrbrmstr) & Jay Jacobs (@jayjacobs)
  License: MIT + file LICENSE

  Slackr contains functions that make it possible to interact with
  Slack.com messaging platform. When you need to share
  information/data from R, rather than resort to copy/paste in e-mails
  or other services like Skype, you can use this package to send
  well-formatted output from multiple R objects and expressions to all
  teammates at the same time with little effort. You can also send
  images from the current graphics device, R objects (as RData), and
  upload files.

* tlm (0.1.2)
  Maintainer: Jose Barrera-Gomez
  Author(s): Jose Barrera-Gomez and Xavier Basagana
  License: GPL (>= 2)

  Computation of effects under linear, logistic and Poisson regression
  models with transformed variables. Logarithm and power
  transformations are allowed. Effects can be displayed both
  numerically and graphically in both the original and the transformed
  space of the variables.

* treatSens (1.0)
  Maintainer: "Nicole Bohme Carnegie"
  Author(s): Nicole Bohme Carnegie, Masataka Harada, Jennifer Hill
  License: GPL-2

  Utilities to investigate sensitivity to unmeasured confounding in
  parametric models with either binary or continuous treatment.

* vcrpart (0.2-1)
  Maintainer: Reto Buergin
  Author(s): Reto Buergin [aut, cre, cph], Gilbert Ritschard [ctb, ths]
  License: GPL (>= 2)

  Recursive partitioning algorithm for varying coefficient generalized
  linear models and ordinal 2-stage linear mixed models. Special
  features are coefficient-wise partitioning, non-varying coefficients
  and partitioning of time-varying variables in longitudinal ordinal

Updated packages

anacor (1.0-5), astro (1.2), BMA (3.18), bpkde (1.0-7), caTools
(1.17.1), catR (3.2), DatABEL (0.9-5), dismo (1.0-5), doBy (4.5-11),
easyanova (4.0), emulator (1.2-15), FastPCS (0.1.0), FastRCS (0.0.4),
fcros (1.2), fpc (2.1-8), gdsfmt (1.1.0), geepack (1.2-0), geosphere
(1.3-11), GGMselect (0.1-9), glmmLasso (1.3.3), glmmLasso (1.3.2), HH
(3.1-5), Hmisc (3.14-5), hwriter (1.3.2), iBATCGH (1.1), ibd (1.2),
intsvy (1.4), investr (1.1.1), isotone (1.0-2), Lahman (3.0-1), lcmm
(1.6.6), MarkedPointProcess (0.2.22), meta (3.8-0), mmcm (1.2-5),
Mobilize (2.16-4), MODISTools (0.94.4), MTurkR (0.5.1), ngspatial
(1.0-4), Ohmage (2.11-4), OjaNP (0.9-8), operators (0.1-7), partykit
(0.8-2), partykit (0.8-1), pbkrtest (0.4-1), PReMiuM (3.0.29), PReMiuM
(3.0.30), rChoiceDialogs (1.0.6), RcmdrPlugin.EBM (1.0-8),
RcmdrPlugin.IPSUR (0.2-1), recosystem (0.2.3), recosystem (0.2.4), rgl
(0.94.1131), RGraphics (2.0-12), seewave (1.7.6), segmented (0.5-0.0),
Sim.DiffProc (2.9), SimComp (2.2), snpEnrichment (1.4-1), spam
(1.0-1), synbreed (0.10-2), TAM (1.0-3.18-1), taxize (0.4.0), TripleR
(1.4), VennDiagram (1.6.8), xtable (1.7-4)

New reviews

* XLConnect, by tim_lindgren

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