CRAN (and crantastic) updates this week
New packages
------------
* EffectStars (1.0)
Maintainer: Unknown
Author(s): Gunther Schauberger
License: GPL-2
http://crantastic.org/packages/EffectStars
The package provides functions to visualize regression models with
categorical response. The effects of the covariates are plotted with
star plots in order to allow for an optical impression of the fitted
model.
* extraBinomial (2.0)
Maintainer: Xin Yang
Author(s): Xin Yang
License: GPL-3
http://crantastic.org/packages/extraBinomial
This package tests for differences in minor allele frequency between
groups and is based on an extra-binomial variation model for pooled
sequencing data. A set of simulated pooled sequencing data can be
generated using this package.
* Familias (1.0)
Maintainer: Petter Mostad
Author(s): Petter Mostad <mostad at chalmers.se>
License: GPL-2
http://crantastic.org/packages/Familias
This package represents a bare-bones implementation of an interface to
the core Familias functions (www.familias.name), which are
programmed in C++. The package itself functions as a kind of
database, where information about persons, pedigrees, allele systems
and observations for persons are entered stepwise. In the end,
probability calculations are made.
* JPSurv (1.0.1)
Maintainer: Yongwu Shao
Author(s): Yongwu Shao <ywshao at gmail.com>,
License: GPL (>= 2)
http://crantastic.org/packages/JPSurv
Functions, methods, and datasets for cancer survival analysis,
including the proportional hazard relative survival model, the join
point relative survival model.
* kappaSize (1.0)
Maintainer: Michael A Rotondi
Author(s): Michael A Rotondi <mrotondi at yorku.ca>
License: GPL (>= 2)
http://crantastic.org/packages/kappaSize
This package contains basic tools for the purpose of sample size
estimation in studies of interobserver/interrater agreement
(reliability). This package contains sample size estimation
functions for both the power-based and confidence interval-based
methods, with binary or multinomial outcomes and two through six
raters.
* koRpus (0.04-27)
Maintainer: m.eik michalke
Author(s): m.eik michalke <meik.michalke at hhu.de>, with contributions
from Earl
Brown <eabrown at csumb.edu>, Alberto Mirisola, and Laura
Hauser
License: GPL (>= 3)
http://crantastic.org/packages/koRpus
A set of tools to analyze texts. Includes, amongst others, functions
for automatic language detection, hyphenation, several indices of
lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and
readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import
functions for language corpora are also provided, to enable
frequency analyses (supports Celex and Leipzig Corpora Collection
file formats). #' Note: For full functionality a local installation
of TreeTagger is recommended. Be encouraged to send feedback to the
author(s)!
* networkDynamic (0.2-2)
Maintainer: Ayn Leslie-Cook
Author(s): Ayn Leslie-Cook, Zack Almquist, Pavel N. Krivitsky, Skye
Bender-deMoll, David R. Hunter, Martina Morris, Carter T.
Butts
License: GPL-3
http://crantastic.org/packages/networkDynamic
Simple interface routines to facilitate the handling of network
objects with complex intertemporal data.
* qLearn (1.0)
Maintainer: Bibhas Chakraborty
Author(s): Jingyi Xin, Bibhas Chakraborty, and Eric B. Laber
License: GPL-2
http://crantastic.org/packages/qLearn
Functions to implement Q-learning for estimating optimal dynamic
treatment regimes from two stage sequentially randomized trials, and
to perform inference via m-out-of-n bootstrap for parameters
indexing the optimal regime.
* Rdistance (1.0)
Maintainer: Trent McDonald
Author(s): Trent McDonald
License: GNU General Public License
http://crantastic.org/packages/Rdistance
Analysis of line transect surveys. Estimates distance-based
sightability functions and abundances.
* relSim (0.1-33)
Maintainer: James M. Curran
Author(s): James M. Curran
License: GPL (>= 2)
http://crantastic.org/packages/relSim
A set of tools to explore the behaviour statistics used for forensic
DNA interpretation when close relatives are involved
* RForcecom (0.1)
Maintainer: Takekatsu Hiramura
Author(s): Takekatsu Hiramura
License: BSD
http://crantastic.org/packages/RForcecom
RForcecom provides the connection to Force.com (Salesforce.com) from
R.
* SAScii (0.1)
Maintainer: Anthony Joseph Damico
Author(s): Anthony Joseph Damico
License: GPL (>= 2)
http://crantastic.org/packages/SAScii
Using any importation code designed for SAS users to read ASCII files
into sas7bdat files, the SAScii package parses through the INPUT
block of a (.sas) syntax file to design the parameters needed for a
read.fwf function call. This allows the user to specify the
location of the ASCII (often a .dat) file and the location of the
.sas syntax file, and then load the data frame directly into R in
just one step.
* sessionTools (0.9-1)
Maintainer: Matthew D. Furia
Author(s): Matthew D. Furia <matt.furia at sagebase.org>
License: GPL-3
http://crantastic.org/packages/sessionTools
This package builds on the save.session function by making installed
packages, options and search paths savable and restorable.
* shotGroups (0.1)
Maintainer: Daniel Wollschlaeger
Author(s): Daniel Wollschlaeger
License: GPL (>= 2)
http://crantastic.org/packages/shotGroups
Analyzes shot group data: Read in data, plot, describe, and compare
shot groups. Perform statistical tests including standard,
nonparametric, and robust methods. Works with files exported by
OnTarget PC and OnTarget TDS.
* TTAinterfaceTrendAnalysis (1.0)
Maintainer: David Devreker
Author(s): David Devreker [aut, cre]
License: GPL (>= 2)
http://crantastic.org/packages/TTAinterfaceTrendAnalysis
This interface was created to develop a standard procedure of temporal
trend analysis in the framework of the OSPAR convention. It is
based on 5 successive steps : chossing and simply manipulate your
database, select the parameters you want to analyse, build your
regulated time series, perform analysis and read the results all in
one easy to use interface. Statistical analysis call other package
function such as Kendall tests (wq package) or cusum function
(Pastec package).
Updated packages
----------------
bnlearn (2.9), catspec (0.96), cda (1.1.3), clue (0.3-44), coin
(1.0-21), crs (0.15-13), cvTools (0.3.0), Deducer (0.6-2),
directlabels (2.4), doRNG (1.2.1), dplR (1.5.3), DSL (0.1-1), eqtl
(1.1-7), ergm (3.0-1), ergm.userterms (3.0-1), fda.usc (0.9.6),
frailtypack (2.2-22), games (1.0-5), gdsfmt (0.9.6), geosphere
(1.2-27), GeoXp (1.5.6), GLDEX (1.0.4.3), gMCP (0.7-8), GSM (1.3),
hive (0.1-14), HLMdiag (0.1.5), HumMeth27QCReport (1.2.13), ibr
(1.4.1), LaplacesDemon (12.03.05), lattice (0.20-5), lattice (0.20-6),
lifecontingencies (0.9.1), lifecontingencies (0.9), lubridate (1.1.0),
Mangrove (1.1), matrixStats (0.4.4), maxLik (1.1-2), meboot (1.1-4),
MHadaptive (1.1-7), miRtest (1.2), mondate (0.9.9.03), multcomp
(1.2-12), multitable (1.3), MVA (1.0-3), networkDynamic (0.2-2), np
(0.40-13), npRmpi (0.40-13), openair (0.5-23), OpenCL (0.1-2),
pheatmap (0.6.1), pks (0.2-0), planar (1.2), plotGoogleMaps (1.2),
PowerTOST (0.9-4), ppstat (0.8), pROC (1.5.1), PTAk (1.2-5), qgraph
(1.0.2), qtl (1.23-16), rbamtools (2.0), rconifers (1.0.7),
RcppArmadillo (0.2.36), readBrukerFlexData (1.2.5), readBrukerFlexData
(1.2.7), readMzXmlData (2.2.1), REGENT (1.0.4), regress (1.3-7),
relevent (1.0-2), Renext (2.0-0), rmongodb (1.0.3), rngSetSeed
(0.2-3), RODBC (1.3-5), RSEIS (3.0-1), rworldmap (0.1300),
sampleSelection (0.7-0), skmeans (0.2-1), Snowball (0.0-8), SNPRelate
(0.9.3), soiltexture (1.2.9), soobench (1.0-73), sp (0.9-97),
SpatioTemporal (0.9.2), SPOT (1.0.2257), support.CEs (0.2-1),
tabuSearch (1.1), tdthap (1.1-3), textir (1.8-2), timsac (1.2.6),
tm.plugin.dc (0.2-1), twang (1.2-5), XLConnect (0.1-9)
New reviews
-----------
* quantmod, by atomicules
http://crantastic.org/reviews/143
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.
CRAN (and crantastic) updates this week
New packages
------------
* bigdata (0.1)
Maintainer: Han Liu
Author(s): Han Liu, Tuo Zhao
License: GPL-2
http://crantastic.org/packages/bigdata
The big data package is a collection of scalable methods for
large-scale data analysis.
* boss (1.0)
Maintainer: Arend Voorman
Author(s): Arend Voorman
License: GPL (>= 2)
http://crantastic.org/packages/boss
BOSS uses parameter estimates obtained without genotype to boost
standard one-step approximations, and precomputes as much as
possible without genotype (using boss.set) to minimize effort
required.
* Distance (0.6)
Maintainer: David L Miller
Author(s): David L. Miller
License: GPL (>= 2)
http://crantastic.org/packages/Distance
A library that provides a simple way of fitting detection functions to
distance sampling data for both line and point transects.
Adjustment term selection, left and right truncation as well as
monotonicity constraints and binning are supported. Abundance and
density estimates can also be calculated if survey area information
is provided.
* FinAsym (1.0)
Maintainer: Paolo Zagaglia
Author(s): Paolo Zagaglia
License: GPL-3
http://crantastic.org/packages/FinAsym
This package accomplishes two tasks: a) it classifies implicit trading
activity from quotes in OTC markets using the algorithm of Lee and
Ready (1991); b) based on information for trade initiation, the
package computes the probability of informed trading of Easley and
O'Hara (1987).
* gammSlice (1.2-5)
Maintainer: Tung Pham
Author(s): Tung Pham and Matt Wand
License: GPL (>= 2)
http://crantastic.org/packages/gammSlice
Uses a slice sampling-based Markov chain Monte Carlo to conduct
Bayesian fitting and inference for generalized additive mixed models
(GAMM). Generalized linear mixed models and generalized additive
models are also handled as special cases of GAMM.
* GenOrd (1.0.1)
Maintainer: Alessandro Barbiero
Author(s): Alessandro Barbiero, Pier Alda Ferrari
License: GPL
http://crantastic.org/packages/GenOrd
The package implements a procedure for generating samples from
ordinal/discrete random variables with pre-specified correlation
matrix and marginal distributions.
* Lambda4 (1.0)
Maintainer: Unknown
Author(s): Tyler Hunt
License: GPL (>= 2)
http://crantastic.org/packages/Lambda4
This code provides 4 different estimates of maximized lambda4 (A split
half reliability estimate)
* leapp (1.0)
Maintainer: Yunting Sun
Author(s): Yunting Sun <yuntings at stanford.edu> , Nancy R.Zhang
<nzhang at stanford.edu>, Art B.Owen <owen at
stanford.edu>
License: GPL (>= 2)
http://crantastic.org/packages/leapp
These functions take a gene expression value matrix, a primary
covariate vector, an additional known covariates matrix. A two
stage analysis is applied to counter the effects of latent variables
on the rankings of hypotheses. The estimation and adjustment of
latent effects are proposed by Sun, Zhang and Owen (2011).
"leapp"
is developed in the context of microarray experiments, but may be
used as a general tool for high throughput data sets where
dependence may be involved.
* lxb (1.1)
Maintainer: Bj??rn Winckler
Author(s): Bj??rn Winckler <bjorn.winckler at gmail.com>
License: BSD
http://crantastic.org/packages/lxb
Functions to quickly read LXB parameter data.
* markdown (0.3)
Maintainer: JJ Allaire
Author(s): JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
License: GPL-3
http://crantastic.org/packages/markdown
Markdown is a plain-text formatting syntax that can be converted to
XHTML or other formats. This package provides R bindings to the
Sundown markdown rendering library.
* phenology (3.28)
Maintainer: Marc Girondot
Author(s): Marc Girondot
License: GPL-2
http://crantastic.org/packages/phenology
Functions to fit and test the phenology of species based on counts.
* RAFM (1.0)
Maintainer: Unknown
Author(s): Markku Karhunen, Uni. Helsinki
License: GPL-2
http://crantastic.org/packages/RAFM
Fits AFM by Metropolis-Hastings, calculates theta and FST out of AFM
parameters
* SCMA (0.0)
Maintainer: Isis Bulte
Author(s): Isis Bulte and Patrick Onghena
License: GPL (>= 2)
http://crantastic.org/packages/SCMA
A package for probability combining (additive and multiplicative
method) and for calculating some effect size measures on single-case
data (SMD, PND and PEM).
* skewtools (0.1.0)
Maintainer: Javier E. Contreras-Reyes
Author(s): Javier E. Contreras-Reyes
License: GPL (>= 2)
http://crantastic.org/packages/skewtools
This package include functions related to following topics: 1.
Information Theory: Entropy and Mutual Informacion Index for
Multivariate Skew-t and Skew-Normal distributions. 2. Estimation of
Growth models parameters (Von Bertalanffy, Gompertz, Logistic and
Richards) using the robust ECME method via Heteroscedastic Nonlinear
Regression Growth model with scale mixture of Skew-Normal
distributions (Normal, T-Student, Skew-Normal and Skew-t). Include
Bootstrap and Jackknife methods to estimate the Variance-Covariance
matrix and Local Influence
* svKomodo (0.9-55)
Maintainer: Philippe Grosjean
Author(s): Philippe Grosjean
License: GPL-2
http://crantastic.org/packages/svKomodo
Functions to manage the GUI client, like Komodo with the SciViews-K
extension
* tempdisagg (0.12)
Maintainer: Christoph Sax
Author(s): Christoph Sax, Peter Steiner
License: GPL-3
http://crantastic.org/packages/tempdisagg
Temporal disaggregation methods are used to disaggregate and
interpolate a low frequency time series to a higher frequency
series. This can be done without additional information or by
exploiting the information contained in one or more indicators. All
disaggregation methods ensure that either the sum, the average, the
first or the last value of the resulting high frequency series is
consistent with the low frequency series.
* TUWmodel (0.1-0)
Maintainer: Alberto Viglione
Author(s): Juraj Parajka, Alberto Viglione
License: GPL (>= 2)
http://crantastic.org/packages/TUWmodel
The model is a lumped conceptual rainfall-runoff model, following the
structure of the HBV model. The model runs on a daily time step and
consists of a snow routine, a soil moisture routine and a flow
routing routine. See Parajka, J., R. Merz, G. Bloeschl (2007)
Uncertainty and multiple objective calibration in regional water
balance modelling: case study in 320 Austrian catchments,
Hydrological Processes, 21, 435-446.
Updated packages
----------------
abd (0.2-2), acepack (1.3-3.1), agricolae (1.1-1), analogue (0.8-2),
ape (3.0-2), apsrtable (0.8-8), aroma.apd (0.2.2), arulesViz (0.1-5),
BHH2 (2012.04-0), bootstrap (2012.04-0), changeLOS (2.1),
clusterGeneration (1.2.9), cmm (0.4), cocorresp (0.2-0), coda
(0.14-7), corpora (0.4-3), ctarma (0.1.2), cts (1.0-10), dbEmpLikeGOF
(1.2.2), deldir (0.0-17), denstrip (1.5.2), DEoptim (2.2-0), difR
(4.2), directlabels (2.5), diveMove (1.3.3), DoseFinding (0.6-2), epiR
(0.9-40), etm (0.5-4), evaluate (0.4.2), evaluate (0.4.1.1), Fahrmeir
(2012.04-0), fdth (1.1-7), FNN (0.6-3), forecast (3.20), formatR
(0.4), fortunes (1.5-0), frailtypack (2.2-23), GDD (0.1-13.1), gldist
(2160.2), gooJSON (1.0.01), gsubfn (0.6-3), gWidgets (0.0-50),
gWidgetsRGtk2 (0.0-80), gWidgetstcltk (0.0-49), hapassoc (1.2-5),
iGenomicViewer (2.4.8), indicspecies (1.6.2), informR (1.0.04), isocir
(1.1), LaplacesDemon (12.04.02), lazyWeave (2.1.3), lmm (0.5), lordif
(0.2-2), meta (2.0-1), metaLik (0.3), mirt (0.2.1), mixOmics (4.0-1),
mixtools (0.4.5), MplusAutomation (0.5-1), msr (0.4), mvna (1.2-2),
nsRFA (0.7-3), oce (0.8-7), OpenRepGrid (0.1.6), optmatch (0.7-3),
PairedData (0.9.1), paleoTS (0.4-3), PearsonDS (0.93), permute
(0.7-0), pgfSweave (1.3.0), phangorn (1.6-0), phmm (0.7-4), pmml
(1.2.30), pomp (0.41-1), PowerTOST (0.9-8), QTLRel (0.2-11), R.cache
(0.6.2), race (0.1.59), raster (1.9-82), rfishbase (0.0-8), rgr
(1.1.5), RMAWGEN (1.2.4), RNCEP (1.0.4), RNiftyReg (0.6.2), rrBLUP
(3.6), RSurvey (0.7-0), RTAQ (0.2), RTextTools (1.3.7), sampSurf
(0.6-2), ScottKnott (1.1-3), seewave (1.6.2), sendplot (3.8.10),
SenSrivastava (2012-04-0), simba (0.3-4), spgwr (0.6-14), StatMatch
(1.0.5), svDialogs (0.9-50), svDialogs (0.9-52), tables (0.6), tau
(0.0-13), textir (1.8-4), TinnR (1.0-5), tis (1.19), tmle (1.2),
treemap (1.0-4), UsingR (0.1-18), vegdata (0.5.7), x12 (1.0-0), yaml
(2.1.4), YourCast (1.5-1), Zelig (3.5.5), zipfR (0.6-6)
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.