Wed, 20 May 2015

Package qdapDictionaries updated to version 1.0.6 with previous version 1.0.5 dated 2015-04-06

Title: Dictionaries and Word Lists for the 'qdap' Package
Description: A collection of dictionaries and word lists for use with the 'qdap' package.
Author: Tyler Rinker
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between qdapDictionaries versions 1.0.5 dated 2015-04-06 and 1.0.6 dated 2015-05-20

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Package ecp updated to version 2.0.0 with previous version 1.6.2 dated 2015-01-04

Title: Non-Parametric Multiple Change-Point Analysis of Multivariate Data
Description: Implements various procedures for finding multiple change-points through the use of U-statistics. The procedures do not make any distributional assumptions other than the existence of certain absolute moments. Hierarchical and exact search methods are included. All methods return the set of estimated change-points as well as other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James <nj89@cornell.edu>

Diff between ecp versions 1.6.2 dated 2015-01-04 and 2.0.0 dated 2015-05-20

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Package xtermStyle updated to version 3.0.5 with previous version 2.2-4 dated 2012-07-19

Title: Terminal Text Formatting Using Escape Sequences
Description: Can be used for coloring output in terminals. It was developed for the standard Ubuntu terminal but should be compatible with any terminal using xterm or ANSI escape sequences. If run in windows, RStudio, or any other platform not supporting such escape sequences it gracefully passes on any output without modifying it.
Author: Christofer Backlin [aut, cre]
Maintainer: Christofer Backlin <christofer.backlin@medsci.uu.se>

Diff between xtermStyle versions 2.2-4 dated 2012-07-19 and 3.0.5 dated 2015-05-20

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Package sirt updated to version 1.6-0 with previous version 1.5-0 dated 2015-03-03

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R, including multidimensional compensatory and noncompensatory IRT models, MCMC for hierarchical IRT models and testlet models, NOHARM, faceted and hierarchical rater models, ordinal IRT model (ISOP), discrete grade of membership model, latent regression models, DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between sirt versions 1.5-0 dated 2015-03-03 and 1.6-0 dated 2015-05-20

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Package oce updated to version 0.9-16 with previous version 0.9-14 dated 2014-05-19

Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including ADCP measurements, CTD measurements, sectional data, sea-level time series, coastline files, etc. Handles dozens of specialized functions for calculating seawater properties such as potential temperature and density, as well as derived properties such as buoyancy frequency and dynamic height. Map projections are calculated using PROJ.4 functions included within the oce.
Author: Dan Kelley [aut, cre], Clark Richards [aut], Chantelle Layton [ctb, cph] (curl() coauthor), Gerald Evenden [ctb, cph] (PROJ.4 author), Frank Warmerdam [ctb, cph] (PROJ.4 author), Howard Butler [ctb, cph] (PROJ.4 author), Brent Fraser [ctb, cph] (PROJ.4 contributor), Chris Stuber [ctb, cph] (PROJ.4 contributor), Craig Bruce [ctb, cph] (PROJ.4 contributor), Victor Osipkov [ctb, cph] (PROJ.4 contributor), Andrea Antonello [ctb, cph] (PROJ.4 contributor), Charles Karney [ctb, cph] (PROJ.4 contributor), Karsten Engsager [ctb, cph] (PROJ.4 contributor), Knud Poder [ctb, cph] (PROJ.4 contributor), Robert Gentleman [ctb, cph] (author of approx() code, used in binmapAdp()), Ross Ihaka [ctb, cph] (author of approx() code, used in binmapAdp())
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>

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Permanent link

Package miceadds updated to version 1.2-0 with previous version 1.1-1 dated 2015-02-23

Title: Some Additional Multiple Imputation Functions, Especially for 'mice'
Description: Contains some auxiliary functions for multiple imputation which complements existing functionality in R. In addition to some utility functions, main features include plausible value imputation, multilevel imputation functions, imputation using partial least squares (PLS) for high dimensional predictors, nested multiple imputation, and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between miceadds versions 1.1-1 dated 2015-02-23 and 1.2-0 dated 2015-05-20

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 MD5                                      |   55 +++++++++++++++------
 NAMESPACE                                |   70 +++++++++++++++++++++++---
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More information about miceadds at CRAN
Permanent link

Package lamW updated to version 0.1-1 with previous version 0.0-1 dated 2015-05-19

Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between lamW versions 0.0-1 dated 2015-05-19 and 0.1-1 dated 2015-05-20

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More information about lamW at CRAN
Permanent link

Package kyotil updated to version 2015.5-20 with previous version 2015.2-27 dated 2015-03-04

Title: Utility Functions by Youyi, Krisz and Others
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>

Diff between kyotil versions 2015.2-27 dated 2015-03-04 and 2015.5-20 dated 2015-05-20

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New package evolqg with initial version 0.1-3
Package: evolqg
Type: Package
Title: Tools for Evolutionary Quantitative Genetics
Version: 0.1-3
Date: 2015-05-18
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Depends: R (>= 3.1.0), plyr (>= 1.7.1)
Imports: Rcpp, reshape2, ggplot2, magrittr, tidyr, vegan, ape, phytools, mvtnorm
Suggests: testthat (>= 0.2), foreach, grid, gridExtra, doParallel
LinkingTo: Rcpp
License: MIT + file LICENSE
BugReports: https://github.com/lem-usp/evolqg/issues
NeedsCompilation: yes
Packaged: 2015-05-20 15:12:22 UTC; diogro
Repository: CRAN
Date/Publication: 2015-05-21 00:53:37

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New package VIGoR with initial version 1.0
Package: VIGoR
Type: Package
Title: Variational Bayesian Inference for Genome-Wide Regression
Version: 1.0
Date: 2015-05-18
Author: Akio Onogi and Hiroyoshi Iwata
Maintainer: Akio Onogi <onogiakio@gmail.com>
Description: Conducts linear regression using variational Bayesian inference, particularly optimized for genome-wide association mapping and whole-genome prediction which use a number of DNA markers as the explanatory variables. Provides seven regression models which select the important variables (i.e., the variables related to response variables) among the given explanatory variables in different ways (i.e., model structures).
License: MIT + file LICENSE
Packaged: 2015-05-20 13:20:36 UTC; seisoku
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-20 15:38:58

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Package RInside updated to version 0.2.13 with previous version 0.2.12 dated 2015-01-28

Title: C++ Classes to Embed R in C++ Applications
Description: C++ classes to embed R in C++ applications The 'RInside' packages makes it easier to have "R inside" your C++ application by providing a C++ wrapper class providing the R interpreter. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the eight subdirectories of the examples/ directory of the installed package: standard, mpi (for parallel computing) qt (showing how to embed 'RInside' inside a Qt GUI application), wt (showing how to build a "web-application" using the Wt toolkit), armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' use with 'RcppEigen'). The example use GNUmakefile(s) with GNU extensions, so a GNU make is required (and will use the GNUmakefile automatically). Doxygen-generated documentation of the C++ classes is available at the 'RInside' website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RInside versions 0.2.12 dated 2015-01-28 and 0.2.13 dated 2015-05-20

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 README.md                    |   29 ++++++++++++++++++++++++-----
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Package mixAK updated to version 4.0-5 with previous version 3.10 dated 2015-02-06

Title: Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between mixAK versions 3.10 dated 2015-02-06 and 4.0-5 dated 2015-05-20

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 NAMESPACE                                  |    5 
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 86 files changed, 2971 insertions(+), 1544 deletions(-)

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Package kml updated to version 2.3 with previous version 2.2 dated 2014-03-24

Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design to cluster longitudinal data. It provides facilities to deal with missing value, compute several quality criterion (Calinski and Harabatz, Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut], Bruno Falissard [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>

Diff between kml versions 2.2 dated 2014-03-24 and 2.3 dated 2015-05-20

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New package ClustMMDD with initial version 1.0.0
Package: ClustMMDD
Type: Package
Title: Variable Selection in Clustering by Mixture Models for Discrete Data
Version: 1.0.0
Date: 2015-05-18
Author: Wilson Toussile
Maintainer: Wilson Toussile <wilson.toussile@gmail.com>
Description: An implementation of a variable selection procedure in clustering by mixture of multinomial models for discrete data. Genotype data are examples of such data with two unordered observations (alleles) at each locus for diploid individual. The two-fold problem is seen as a model selection problem where competing models are characterized by the number of clusters K, and the subset S of clustering variables. Competing models are compared by penalized maximum likelihood criteria. We considered asymptotic criteria such as Akaike and Bayesian Information criteria, and a family of penalized criteria with penalty function to be data driven calibrated.
License: GPL (>= 2)
Depends: Rcpp (>= 0.11.5)
Collate: "RcppExports.R" "ClustMMDD.R" "modelKS.R" "zzz.R"
LazyLoad: true
Imports: methods
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2015-05-20 12:59:33 UTC; tousswil
Repository: CRAN
Date/Publication: 2015-05-20 15:19:27

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New package CausalFX with initial version 1.0.1
Package: CausalFX
Type: Package
Title: Methods for Estimating Causal Effects from Observational Data
Version: 1.0.1
Date: 2015-05-20
Imports: igraph, rcdd, rje
Authors@R: c(person("Ricardo", "Silva", email = "ricardo@stats.ucl.ac.uk", role = c("cre", "aut")), person("Robin", "Evans", email = "robin.evans@stats.ox.ac.uk", role = "aut"))
Maintainer: Ricardo Silva <ricardo@stats.ucl.ac.uk>
Description: Estimate causal effects of one variable on another, currently for binary data only. Methods include instrumental variable bounds, adjustment by a given covariate set, adjustment by an induced covariate set using a variation of the PC algorithm, and an effect bounding method (the Witness Protection Program) based on covariate adjustment with observable independence constraints.
License: GPL (>= 2)
URL: http://github.com/rbas2015/CausalFX
BugReports: http://github.com/rbas2015/CausalFX/issues
NeedsCompilation: no
Packaged: 2015-05-20 14:22:42 UTC; ricardo
Author: Ricardo Silva [cre, aut], Robin Evans [aut]
Repository: CRAN
Date/Publication: 2015-05-20 17:10:47

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New package SubpathwayGMir with initial version 1.0
Package: SubpathwayGMir
Type: Package
Title: Identify Metabolic Subpathways Mediated by MicroRNAs
Version: 1.0
Date: 2015-05-20
Author: Li Feng, Chunquan Li and Xia Li
Maintainer: Li Feng <biofengfeng@sina.com>
Description: Routines for identifying metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through converting KEGG metabolic pathways to graphs with genes as nodes and compounds as edges, and then integrating miRNA-target interactions verified by low-throughput experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease) into converted pathway graphs. (2) This package can locate metabolic subpathways mediated by miRNAs by topologically analyzing the "lenient distance" of miRNAs and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can identify significantly enriched miRNA-mediated metabolic subpathways based on located subpathways by hypergenomic test. (4) This package can support six species for metabolic subpathway identification, such as caenorhabditis elegans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and user only need to update interested organism-specific environment variables.
Depends: R (>= 3.0.2), XML, igraph
Collate: fdr.est.R getBackground.R getEdgeLabel.R getEdgeLty.R getInteGraphList.R GetK2riData.R getLayout.R getLocSubGraph.R getOneNodePath.R getSymbolFromGene.R identifyGraph.R initializeK2ri.R plotGraph.R printGraph.R updateOrgEnvir.R mytriangle.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Annotation, SubPathways, Graphs, MicroRNAs
Packaged: 2015-05-20 06:50:06 UTC; sunyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-20 14:15:38

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Package shapeR updated to version 0.1-5 with previous version 0.1-3 dated 2015-04-03

Title: Collection and Analysis of Otolith Shape Data
Description: Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.
Author: Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
Maintainer: Lisa Anne Libungan <lisa.libungan@gmail.com>

Diff between shapeR versions 0.1-3 dated 2015-04-03 and 0.1-5 dated 2015-05-20

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Package ruv updated to version 0.9.5 with previous version 0.9.4 dated 2014-10-24

Title: Detect and Remove Unwanted Variation using Negative Controls
Description: Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', and 'RUV-rinv', along with various supporting algorithms.
Author: Johann Gagnon-Bartsch <johann@stat.berkeley.edu>
Maintainer: Johann Gagnon-Bartsch <johann@stat.berkeley.edu>

Diff between ruv versions 0.9.4 dated 2014-10-24 and 0.9.5 dated 2015-05-20

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Package emil updated to version 2.0.2 with previous version 1.1-6 dated 2014-08-01

Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with resampling methods. The aim of this package is to provide a simple and efficient general framework for working with any type of prediction problem, be it classification, regression or survival analysis, that is easy to extend and adapt to your specific setting. Some commonly used methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre], Mats Gustafsson [aut]
Maintainer: Christofer Backlin <christofer.backlin@medsci.uu.se>

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Permanent link

New package covr with initial version 1.0.0
Package: covr
Title: Test Coverage for Packages
Version: 1.0.0
Authors@R: person("Jim", "Hester", email = "james.f.hester@gmail.com", role = c("aut", "cre"))
Description: Track and report code coverage for your package and (optionally) upload the results to a coverage service like Codecov (http://codecov.io) or Coveralls (http://coveralls.io). Code coverage is a measure of the amount of code being exercised by the tests. It is an indirect measure of test quality. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/Fortran code.
Depends: R (>= 3.1.0), methods
Imports: jsonlite, rex, devtools, httr, crayon, htmltools
Suggests: R6, knitr, shiny (>= 0.11.1), testthat, rstudioapi (>= 0.2)
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2015-05-19 16:05:52 UTC; jhester
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-20 09:18:33

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Package TickExec updated to version 1.1 with previous version 1.0 dated 2015-04-22

Title: Execution Functions for Tick Data Back Test
Description: Functions to execute orders in backtesting using tick data. A testing platform was established by the four major execution functions, namely 'LimitBuy', 'LimitSell', 'MarketBuy' and 'MarketSell', which enclosed all tedious aspects (such as queueing for order executions and calculate actual executed volumes) for order execution using tick data. Such that one can focus on the logic of strategies, rather than its execution.
Author: HKUST
Maintainer: SONG Yang <ysongad@connect.ust.hk>

Diff between TickExec versions 1.0 dated 2015-04-22 and 1.1 dated 2015-05-20

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Package DLMtool updated to version 1.35 with previous version 1.34 dated 2014-09-14

Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>

Diff between DLMtool versions 1.34 dated 2014-09-14 and 1.35 dated 2015-05-20

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