[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
http://crantastic.org/packages/anim-plots
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
http://crantastic.org/packages/aoos
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
object.
* CpGFilter (1.0)
Maintainer: Jun Chen
Author(s): Jun Chen
License: GPL-2
http://crantastic.org/packages/CpGFilter
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
http://crantastic.org/packages/dfcomb
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
http://crantastic.org/packages/dfmta
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,
2014.
* dummy (0.1.0)
Maintainer: Michel Ballings
Author(s): Michel Ballings and Dirk Van den Poel
License: GPL (>= 2)
http://crantastic.org/packages/dummy
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)
http://crantastic.org/packages/FAMILY
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)
http://crantastic.org/packages/geesmv
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
http://crantastic.org/packages/geocodeHERE
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
http://crantastic.org/packages/ggswissmaps
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
http://crantastic.org/packages/hcp
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
http://crantastic.org/packages/heritability
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
thaliana.
* ionflows (1.0)
Maintainer: Michael Bockmayr
Author(s): Michael Bockmayr and Jan Budczies
License: GPL-3
http://crantastic.org/packages/ionflows
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
http://crantastic.org/packages/LinCal
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)
http://crantastic.org/packages/lpme
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)
http://crantastic.org/packages/MGL
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
http://crantastic.org/packages/OptionPricing
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
http://crantastic.org/packages/PANDA
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
http://crantastic.org/packages/pez
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
http://crantastic.org/packages/PLSbiplot1
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
http://crantastic.org/packages/poplite
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)
http://crantastic.org/packages/prc
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)
http://crantastic.org/packages/ScoreGGUM
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
http://crantastic.org/packages/sdcTarget
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
http://crantastic.org/packages/snht
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
http://crantastic.org/packages/spareserver
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)
http://crantastic.org/packages/sudokuAlt
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)
http://crantastic.org/packages/TRSbook
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)
http://crantastic.org/packages/Watersheds
Methods for watersheds aggregation and spatial drainage network
analysis.
* WhiteStripe (1.0)
Maintainer: John Muschelli
Author(s): Taki Shinohara, John Muschelli
License: GPL-2
http://crantastic.org/packages/WhiteStripe
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)
http://crantastic.org/packages/wikipediatrend
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
http://crantastic.org/packages/xtal
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 (1.5.5.1), lpSolveAPI
(5.5.2.0-12), marelac (2.1.4), marmap (0.9), MAT (2.2), MGL (1.1),
msgl (2.0.125.1), 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 (1.6.5.1),
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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