[R] CRAN (and crantastic) updates this week
Crantastic
cranatic at gmail.com
Mon Oct 20 00:40:06 CEST 2014
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.schuwirth at eawag.ch> and Peter Reichert
<peter.reichert at 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.ehrlinger at 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.donoghoe at 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.10 at 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: "Gabor Csardi"
Author(s): "Gabor Csardi" [aut, cre]
License: MIT + file LICENSE
http://crantastic.org/packages/prettyunits
Pretty, human readable formatting of quantities. Time intervals:
1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a
month ago. Bytes: 1337 -> 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 <edd at 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 <rkirkpatrick2 at 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 <khyuns at 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: "Gabor Csardi"
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)
This email provided as a service for the R community by
http://crantastic.org.
Like it? Hate it? Please let us know: cranatic at gmail.com.
More information about the R-help
mailing list