Sat, 23 May 2015

New package restimizeapi with initial version 1.0.0
Package: restimizeapi
Type: Package
Title: Functions for Working with the 'www.estimize.com' Web Services
Version: 1.0.0
Date: 2015-05-23
Author: Thomas P. Fuller <thomas.fuller@coherentlogic.com>
Maintainer: Thomas P. Fuller <thomas.fuller@coherentlogic.com>
Description: Provides the user with functions to develop their trading strategy, uncover actionable trading ideas, and monitor consensus shifts with crowdsourced earnings and economic estimate data directly from <www.estimize.com>. Further information regarding the web services this package invokes can be found at <www.estimize.com/api>.
Depends: R (>= 3.1.3), RCurl, RJSONIO
Suggests: testthat
SystemRequirements:
LazyLoad: yes
License: LGPL-3
Copyright: (C) 2015 Coherent Logic Limited; ALL RIGHTS RESERVED.
URL: http://www.r-project.org, http://coherentlogic.com/middleware-development/r-package-for-the-estimize-com-api?source=cran, https://www.estimize.com?source=cran
Repository: CRAN
Archs: i386, x64
Packaged: 2015-05-22 18:57:15 UTC; thospfuller
NeedsCompilation: no
Date/Publication: 2015-05-23 08:55:19

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Fri, 22 May 2015

New package mitml with initial version 0.2-2
Package: mitml
Type: Package
Title: Tools for Multiple Imputation in Multilevel Modeling
Version: 0.2-2
Date: 2015-05-23
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Imports: pan, haven
Suggests: lme4, nlme, mice
LazyData: true
LazyLoad: true
Description: Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the 'pan' package, and several functions for visualization, data management and the analysis of multiply imputed data sets.
License: GPL (>= 2)
Packaged: 2015-05-22 22:08:44 UTC; simon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-23 01:34:51

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New package Gotoh with initial version 0.9
Package: Gotoh
Type: Package
Title: C++ Wrapper for R which Does Alignments using Gotoh Algorithm
Version: 0.9
Date: 2015-05-18
Author: Rafael Nozal Canyadas <rca025@uib.no> , Eivind Valen <eivind.valen@gmail.com>
Maintainer: Rafael Nozal Canyadas <rca025@uib.no>
Description: Implement a Gotoh approach to sequence alignment. The Gotoh algorithm was first published by Osamu Gotoh in 1982; for more information please refer to: <doi:10.1016/0022-2836(82)90398-9> We are using 'Rcpp', which decrease greatly the CPU time with respect other alignment implementations. This was done in an effort to speed up the calculations for the project AmpliCan. The improvement we got compared with 'DECIPHER' is in between 300x and 500x many fold for sequences between 100 to 200 nucleotides, and between 100x and 200x for sequences of between 200 to 300 nucleotides. And up to 1.5x for sequences of size 10.000 nucleotides and beyond. This package contains the minimum files require for it to work. Please download the repository at: https://rafanozal@bitbucket.org/rafanozal/amplican.git to get the a more verbose documentation and script benchmarks.
Depends: R (>= 3.1.1)
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp
Packaged: 2015-05-22 19:21:41 UTC; rafaelc
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-22 22:39:20

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New package dpmr with initial version 0.1.7-1
Package: dpmr
Title: Data Package Manager for R
Description: Create, install, and summarise data packages that follow the Open Knowledge Foundation's Data Package Protocol.
Version: 0.1.7-1
Date: 2015-05-22
Authors@R: c( person("Christopher", "Gandrud", email = "christopher.gandrud@gmail.com", role = c("aut", "cre")) )
URL: http://christophergandrud.github.io/dpmr/
BugReports: https://github.com/christophergandrud/dpmr/issues
License: GPL-3
Imports: digest, httr, jsonlite, magrittr, rio
Suggests: devtools, testthat
NeedsCompilation: no
Packaged: 2015-05-22 10:22:53 UTC; christophergandrud
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-22 13:22:08

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Thu, 21 May 2015

New package pcaBootPlot with initial version 0.1.0
Package: pcaBootPlot
Title: Create 2D Principal Component Plots with Bootstrapping
Version: 0.1.0
Author: Joshua Starmer
Maintainer: Joshua Starmer <starmer@unc.edu>
Description: Draws a 2D principal component plot using the first 2 principal components from the original and bootstrapped data to give some sense of variability.
Depends: R (>= 3.0.2)
License: GPL-2
LazyData: true
Imports: RColorBrewer
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-05-21 17:37:16 UTC; jstarmer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-21 20:12:06

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New package metagear with initial version 0.1
Package: metagear
Version: 0.1
Date: 2015-05-20
Title: Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis
Authors@R: person("Marc J.", "Lajeunesse", email = "lajeunesse@usf.edu", role = c("aut", "cre"))
Description: Functionalities for facilitating systematic reviews, data extractions, and meta-analyses. It includes a GUI (graphical user interface) to help screen the abstracts and titles of bibliographic data; tools to assign screening effort across multiple collaborators/reviewers and to assess inter-reviewer reliability; tools to help automate the download and retrieval of journal PDF articles from online databases; automated data extractions from scatter-plots; PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools to fill gaps in incomplete or missing study parameters; generation of random effects sizes for Hedges' d, log response ratio, odds ratio, and correlation coefficients for Monte Carlo experiments; covariance equations for modelling dependencies among multiple effect sizes (e.g., effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software. Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031.
Type: Package
Depends: R (>= 3.0.0)
Imports: EBImage (>= 4.4.0), gWidgetsRGtk2 (>= 0.0-83), gWidgets (>= 0.0-54), stringr (>= 0.6.2), metafor (>= 1.9-4), MASS (>= 7.3-29), Matrix (>= 1.1-3)
License: GPL (>= 2)
URL: http://lajeunesse.myweb.usf.edu
Packaged: 2015-05-21 13:01:03 UTC; MJL
Author: Marc J. Lajeunesse [aut, cre]
Maintainer: Marc J. Lajeunesse <lajeunesse@usf.edu>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-21 16:24:43

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New package DAISIE with initial version 1.0
Package: DAISIE
Type: Package
Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Version: 1.0
Date: 2015-05-20
Depends: R (>= 3.0.0), deSolve
Author: Rampal S. Etienne & Luis M. Valente
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
License: GPL-2
Description: Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. 2015. Ecology Letters. In press.
Packaged: 2015-05-20 20:50:22 UTC; p223208
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-21 09:40:32

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Wed, 20 May 2015

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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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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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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Tue, 19 May 2015

New package decisionSupport with initial version 1.101.1
Package: decisionSupport
Type: Package
Title: Quantitative Support of Decision Making under Uncertainty
Version: 1.101.1
Date: 2015-05-19
Authors@R: c( person("Lutz", "Göhring", email = "lutz.goehring@gmx.de", role = c("cre", "aut"), comment="ICRAF and Lutz Göhring Consulting"), person("Eike", "Luedeling", email = "eike@eikeluedeling.com ", role = "aut", comment="ICRAF"))
Copyright: World Agroforestry Centre (ICRAF) 2015
Description: Supporting the quantitative analysis of binary welfare based decision making processes using Monte Carlo simulations. Decision support is given on two levels: (i) The actual decision level is to choose between two alternatives under probabilistic uncertainty. This package calculates the optimal decision based on maximizing expected welfare. (ii) The meta decision level is to allocate resources to reduce the uncertainty in the underlying decision problem, i.e to increase the current information to improve the actual decision making process. This problem is dealt with using the Value of Information Analysis. The Expected Value of Information for arbitrary prospective estimates can be calculated as well as Individual and Clustered Expected Value of Perfect Information. The probabilistic calculations are done via Monte Carlo simulations. This Monte Carlo functionality can be used on its own.
License: GPL-3
Depends: R (>= 3.1.3)
Imports: msm (>= 1.5), mvtnorm (>= 1.0.2), stats (>= 3.1.3)
Suggests: chillR (>= 0.54), eha (>= 2.4.2), mc2d (>= 0.1.15), nleqslv (>= 2.6), pls (>= 2.4.3), rriskDistributions (>= 2.0), testthat (>= 0.9.1), knitr
URL: http://www.worldagroforestry.org/
Encoding: UTF-8
Collate: 'rmvnorm90ci_exact.R' 'rdistq_fit.R' 'random.R' 'paramtnormci_numeric.R' 'paramtnormci_fit.R' 'rtnorm90ci.R' 'rdist90ci_exact.R' 'estimate1d.R' 'estimate.R' 'mcSimulation.R' 'welfareDecisionAnalysis.R' 'eviSimulation.R' 'individualEvpiSimulation.R' 'estimate_read_csv_old.R' 'decisionSupport.R' 'decisionSupport-package.R' 'plainNames2data.frameNames.R' 'plsr.mcSimulation.R'
Packaged: 2015-05-19 18:26:37 UTC; goehring
Author: Lutz Göhring [cre, aut] (ICRAF and Lutz Göhring Consulting), Eike Luedeling [aut] (ICRAF)
Maintainer: Lutz Göhring <lutz.goehring@gmx.de>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-20 01:20:39

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New package clustertend with initial version 1.4
Package: clustertend
Type: Package
Title: Check the Clustering Tendency
Version: 1.4
Date: 2015-05-17
Author: Luo YiLan, Zeng RuTong
Maintainer: Zeng RuTong <670273197@qq.com>
Description: Calculate some statistics aiming to help analyzing the clustering tendency of given data. In the first version, Hopkins' statistic is implemented.
License: GPL (>= 2)
Packaged: 2015-05-19 15:34:31 UTC; dell
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-20 01:15:11

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New package bigml with initial version 0.1.2
Package: bigml
Type: Package
Title: Bindings for the BigML API
Version: 0.1.2
Date: 2015-05-08
Authors@R: c(person("Leon", "Hwang", role=c("cre", "aut"), email="hwang@bigml.com"))
Description: The 'bigml' package contains bindings for the BigML API. The package includes methods that provide straightforward access to basic API functionality, as well as methods that accommodate idiomatic R data types and concepts.
License: LGPL-3
URL: https://github.com/bigmlcom/bigml-r
BugReports: https://github.com/bigmlcom/bigml-r/issues
Imports: RJSONIO, RCurl, plyr
Collate: 'bigml-internal.R' 'formEncodeURL.R' 'bigml-package.R' 'createDataset.R' 'createModel.R' 'createPrediction.R' 'createSource.R' 'getDataset.R' 'getModel.R' 'getPrediction.R' 'getSource.R' 'listDatasets.R' 'listModels.R' 'listSources.R' 'quickDataset.R' 'quickModel.R' 'quickPrediction.R' 'quickSource.R' 'setCredentials.R' 'deleteResource.R'
NeedsCompilation: no
Packaged: 2015-05-19 07:44:35 UTC; leon
Author: Leon Hwang [cre, aut]
Maintainer: Leon Hwang <hwang@bigml.com>
Repository: CRAN
Date/Publication: 2015-05-20 01:18:53

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New package lamW with initial version 0.0-1
Package: lamW
Type: Package
Title: Lambert-W Function
Version: 0.0-1
Date: 2015-05-19
Authors@R: c(person(given="Avraham", family="Adler", role=c("aut", "cph", "cre"), email="Avraham.Adler@gmail.com"))
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.
License: BSD_2_clause + file LICENSE
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp
Suggests: testthat
NeedsCompilation: yes
Packaged: 2015-05-19 20:52:55 UTC; aadler00
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-20 00:19:42

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New package ARTIVA with initial version 1.2.3
Package: ARTIVA
Type: Package
Title: Time-Varying DBN Inference with the ARTIVA (Auto Regressive TIme VArying) Model
Version: 1.2.3
Date: 2015-05-19
Author: S. Lebre and G. Lelandais.
Maintainer: S. Lebre <sophie.lebre@icube.unistra.fr>
Depends: MASS, igraph, gplots
Description: Reversible Jump MCMC (RJ-MCMC)sampling for approximating the posterior distribution of a time varying regulatory network, under the Auto Regressive TIme VArying (ARTIVA) model (for a detailed description of the algorithm, see Lebre et al. BMC Systems Biology, 2010). Starting from time-course gene expression measurements for a gene of interest (referred to as "target gene") and a set of genes (referred to as "parent genes") which may explain the expression of the target gene, the ARTIVA procedure identifies temporal segments for which a set of interactions occur between the "parent genes" and the "target gene". The time points that delimit the different temporal segments are referred to as changepoints (CP).
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2015-05-19 20:18:20 UTC; lebre
Repository: CRAN
NeedsCompilation: no
Date/Publication: 2015-05-20 01:09:27

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New package rriskDistributions with initial version 2.1
Package: rriskDistributions
Type: Package
Title: Fitting Distributions to Given Data or Known Quantiles
Description: Collection of functions for fitting distributions to given data or by known quantiles. Two main functions fit.perc() and fit.cont() provide users a GUI that allows to choose a most appropriate distribution without any knowledge of the R syntax. Note, this package is a part of the 'rrisk' project.
License: GPL (>= 3)
LazyLoad: yes
URL: http://www.bfr.bund.de/cd/52158
Depends: R(>= 2.11.0)
Imports: mc2d, eha, msm, tcltk, tkrplot
SystemRequirements: Tcl/Tk (>= 8.5), Tktable (>= 2.9)
Authors@R: c(person(given="Natalia", family="Belgorodski", email="belgorodski@stat-up.de", role=c("aut"), comment="STAT-UP Statistical Consulting"), person(given="Matthias", family="Greiner", email="matthias.greiner@bfr.bund.de", role=c("aut", "cre"), comment="Federal Institute for Risk Assessment, Germany"), person(given="Kristin", family="Tolksdorf", email="kristin.tolksdorf@bfr.bund.de", role=c("aut"), comment="Federal Institute for Risk Assessment, Germany"), person(given="Katharina", family="Schueller", email="schueller@stat-up.de", role=c("aut"), comment="STAT-UP Statistical Consulting"), person(given="Matthias", family="Flor", email="Matthias.Flor@bfr.bund.de", role=c("ctb"), comment="Federal Institute for Risk Assessment, Germany"), person(given="Lutz", family="Göhring", email="lutz.goehring@gmx.de", role=c("ctb"), comment="Lutz Göhring Consulting"))
Version: 2.1
Date: 2015-05-11
Encoding: UTF-8
Collate: 'rriskDistributions-package.R' 'rriskDistributions_functions_v1.9.1.R'
NeedsCompilation: no
Packaged: 2015-05-13 07:36:13 UTC; flor
Author: Natalia Belgorodski [aut] (STAT-UP Statistical Consulting), Matthias Greiner [aut, cre] (Federal Institute for Risk Assessment, Germany), Kristin Tolksdorf [aut] (Federal Institute for Risk Assessment, Germany), Katharina Schueller [aut] (STAT-UP Statistical Consulting), Matthias Flor [ctb] (Federal Institute for Risk Assessment, Germany), Lutz Göhring [ctb] (Lutz Göhring Consulting)
Maintainer: Matthias Greiner <matthias.greiner@bfr.bund.de>
Repository: CRAN
Date/Publication: 2015-05-19 18:13:53

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New package IATscores with initial version 0.1-2
Package: IATscores
Title: Implicit Association Test Scores Using Robust Statistics
Description: Compute several variations of the Implicit Association Test (IAT) scores, including the D scores (Greenwald, Nosek, Banaji, 2003) and the new scores that were developed using robust statistics (Richetin, Costantini, Perugini, and Schonbrodt, 2015).
Author: Giulio Costantini
Maintainer: Giulio Costantini <costantinigiulio@gmail.com>
Date: 2015-05-18
Version: 0.1-2
Type: Package
Depends: R (>= 3.2.0)
Imports: stringr (>= 0.6.2), dplyr (>= 0.2), reshape2 (>= 1.4), nem (>= 2.38.0), qgraph (>= 1.2.5)
Suggests: nparcomp (>= 2.0)
License: GPL-2
NeedsCompilation: no
Packaged: 2015-05-19 13:41:35 UTC; giulio.costantini
Repository: CRAN
Date/Publication: 2015-05-19 18:03:06

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New package greyzoneSurv with initial version 1.0
Package: greyzoneSurv
Type: Package
Title: Fit a Grey-Zone Model with Survival Data
Version: 1.0
Date: 2015-05-18
Author: Pingping Qu and John Crowley
Maintainer: Pingping Qu <pingpingq@crab.org>
Description: Allows one to classify patients into low, intermediate, and high risk groups for disease progression based on a continuous marker that is associated with progression-free survival. It uses a latent class model to link the marker and survival outcome and produces two cutoffs for the marker to divide patients into three groups. See the References section for more details.
License: GPL-3
Depends: stats4, survival, Hmisc, survAUC
NeedsCompilation: no
Packaged: 2015-05-19 06:40:41 UTC; pingpingq
Repository: CRAN
Date/Publication: 2015-05-19 09:25:40

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New package OpenMx with initial version 2.2.2
Package: OpenMx
Date: 2015-05-18
Title: Extended Structural Equation Modelling
Authors@R: c(person(c("Steven", "M."), "Boker", role="aut"), person(c("Michael", "C."), "Neale", role="aut"), person(c("Hermine", "H."), "Maes", role="aut"), person(c("Michael", "J."), "Wilde", role="ctb"), person("Michael", "Spiegel", role="aut"), person(c("Timothy", "R."), "Brick", role="aut"), person("Ryne", "Estabrook", role="aut"), person(c("Timothy", "C."), "Bates", role="aut"), person("Paras", "Mehta", role="ctb"), person("Timo", c("von", "Oertzen"), role="ctb"), person(c("Ross", "J."), "Gore", role="aut"), person(c("Michael", "D."), "Hunter", role="aut"), person(c("Daniel", "C."), "Hackett", role="ctb"), person("Julian", "Karch", role="ctb"), person(c("Andreas", "M."), "Brandmaier", role="ctb"), person(c("Joshua", "N."), "Pritikin", email="jpritikin@pobox.com", role=c("aut", 'cre')), person("Mahsa", "Zahery", role="aut"), person(c("Robert", "M."), "Kirkpatrick", role="aut"))
URL: http://openmx.psyc.virginia.edu
BugReports: http://openmx.psyc.virginia.edu/forums
Description: Facilitates treatment of statistical model specifications as things that can be generated and manipulated programmatically. Structural equation models may be specified with reticular action model matrices or paths, linear structural relations matrices or paths, or directly in matrix algebra. Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential equations, state space, and many others.
SystemRequirements: GNU make
License: Apache License (== 2.0) | file LICENSE
LinkingTo: RcppEigen, StanHeaders, BH
Depends: R (>= 3.0.2), digest, MASS, methods, parallel
Suggests: Matrix, mvtnorm, numDeriv, roxygen2 (>= 3.1), Rmpi, rpf (>= 0.36), snowfall
LazyLoad: yes
LazyData: yes
Collate: '0ClassUnion.R' 'cache.R' 'MxBaseNamed.R' 'MxData.R' 'MxDataWLS.R' 'DefinitionVars.R' 'MxReservedNames.R' 'MxNamespace.R' 'MxSearchReplace.R' 'MxFlatSearchReplace.R' 'MxUntitled.R' 'MxAlgebraFunctions.R' 'MxExponential.R' 'MxMatrix.R' 'DiagMatrix.R' 'FullMatrix.R' 'IdenMatrix.R' 'LowerMatrix.R' 'SdiagMatrix.R' 'StandMatrix.R' 'SymmMatrix.R' 'UnitMatrix.R' 'ZeroMatrix.R' 'MxMatrixFunctions.R' 'MxAlgebra.R' 'MxCycleDetection.R' 'MxDependencies.R' 'MxAlgebraConvert.R' 'MxAlgebraTransform.R' 'MxSquareBracket.R' 'MxEval.R' 'MxRename.R' 'MxPath.R' 'MxObjectiveMetaData.R' 'MxRAMMetaData.R' 'MxExpectation.R' 'MxExpectationNormal.R' 'MxExpectationRAM.R' 'MxExpectationLISREL.R' 'MxFitFunction.R' 'MxFitFunctionAlgebra.R' 'MxFitFunctionML.R' 'MxFitFunctionMultigroup.R' 'MxFitFunctionRow.R' 'MxFitFunctionWLS.R' 'MxRAMObjective.R' 'MxLISRELObjective.R' 'MxFIMLObjective.R' 'MxMLObjective.R' 'MxRowObjective.R' 'MxAlgebraObjective.R' 'MxBounds.R' 'MxConstraint.R' 'MxInterval.R' 'MxTypes.R' 'MxCompute.R' 'MxModel.R' 'MxRAMModel.R' 'MxLISRELModel.R' 'MxModelDisplay.R' 'MxFlatModel.R' 'MxMultiModel.R' 'MxModelFunctions.R' 'MxModelParameters.R' 'MxUnitTesting.R' 'MxApply.R' 'MxRun.R' 'MxRunHelperFunctions.R' 'MxSummary.R' 'MxCompare.R' 'MxSwift.R' 'MxOptions.R' 'MxThreshold.R' 'OriginalMx.R' 'MxGraph.R' 'MxGraphviz.R' 'MxDeparse.R' 'MxCommunication.R' 'MxRestore.R' 'MxVersion.R' 'MxPPML.R' 'MxRAMtoML.R' 'MxDiff.R' 'MxErrorHandling.R' 'MxDetectCores.R' 'MxSaturatedModel.R' 'omxBrownie.R' 'omxConstrainThresholds.R' 'omxGetNPSOL.R' 'MxFitFunctionR.R' 'MxRObjective.R' 'MxExpectationStateSpace.R' 'MxExpectationBA81.R' 'MxFitFunctionGREML.R' 'MxExpectationGREML.R' 'MxMI.R' 'zzz.R'
Version: 2.2.2
Packaged: 2015-05-18 12:16:23 UTC; joshua
Author: Steven M. Boker [aut], Michael C. Neale [aut], Hermine H. Maes [aut], Michael J. Wilde [ctb], Michael Spiegel [aut], Timothy R. Brick [aut], Ryne Estabrook [aut], Timothy C. Bates [aut], Paras Mehta [ctb], Timo von Oertzen [ctb], Ross J. Gore [aut], Michael D. Hunter [aut], Daniel C. Hackett [ctb], Julian Karch [ctb], Andreas M. Brandmaier [ctb], Joshua N. Pritikin [aut, cre], Mahsa Zahery [aut], Robert M. Kirkpatrick [aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-19 08:53:08

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New package threejs with initial version 0.2.1
Package: threejs
Type: Package
Title: Interactive 3D Scatter Plots and Globes
Description: Create interactive 3D scatter plots and globes using the 'three.js' visualization library ("http://threejs.org").
Version: 0.2.1
Date: 2015-04-24
Author: B. W. Lewis <blewis@illposed.net>
Maintainer: B. W. Lewis <blewis@illposed.net>
URL: http://bwlewis.github.io/rthreejs
License: MIT + file LICENSE
Depends: R (>= 3.0.0)
Imports: htmlwidgets (>= 0.3.2), base64enc
Suggests: htmltools (>= 0.2.6), RCurl, maps, sp
Enhances: knitr, shiny
NeedsCompilation: no
Packaged: 2015-05-19 02:34:45 UTC; blewis
Repository: CRAN
Date/Publication: 2015-05-19 06:13:04

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New package qrmtools with initial version 0.0-1
Package: qrmtools
Version: 0.0-1
Encoding: UTF-8
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from the book "Quantitative Risk Management: Concepts, Techniques and Tools". Furthermore, new developments and auxiliary functions for Quantitative Risk Management practice.
Authors@R: c(person(given = "Marius", family = "Hofert", role = c("aut", "cre"), email = "marius.hofert@uwaterloo.ca"), person(given = "Kurt", family = "Hornik", role = "aut", email = "Kurt.Hornik@R-project.org"))
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Depends: R (>= 3.0.0)
Imports: xts
Suggests:
Enhances:
License: GPL-2 | GPL-3
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-19 06:39:55
Packaged: 2015-05-19 04:23:08 UTC; mhofert

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Mon, 18 May 2015

New package RFgroove with initial version 1.0
Package: RFgroove
Type: Package
Title: Importance Measure and Selection for Groups of Variables with Random Forests
Version: 1.0
Date: 2015-05-13
Author: Baptiste Gregorutti
Maintainer: Baptiste Gregorutti <baptiste.gregorutti@safety-line.fr>
Description: Variable selection tools for groups of variables and functional data based on a new grouped variable importance with random forests.
License: GPL (>= 2.0)
Depends: randomForest, wmtsa, fda
Packaged: 2015-05-18 15:20:18 UTC; bapt
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-19 00:07:20

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New package novelist with initial version 1.0
Package: novelist
Type: Package
Title: NOVEL Integration of the Sample and Thresholded (NOVELIST) Correlation and Covariance Estimators
Version: 1.0
Date: 2015-05-17
Author: Na Huang and Piotr Fryzlewicz
Maintainer: Na Huang <n.huang1@lse.ac.uk>
Depends: R (>= 3.0.2)
Description: Estimate Large correlation and covariance matrices and their inverses using integration of the sample and thresholded correlation and covariance estimators.
License: GPL (>= 3)
Packaged: 2015-05-18 08:54:06 UTC; Qian
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-19 00:14:47

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New package supcluster with initial version 1.0
Package: supcluster
Type: Package
Title: Supervised Cluster Analysis
Version: 1.0
Date: 2015-05-18
Author: David A. Schoenfeld, Jesse Hsu
Maintainer: David A. Schoenfeld <dschoenfeld@mgh.harvard.edu>
Description: Clusters features under the assumption that each cluster has a random effect and there is an outcome variable that is related to the random effects by a linear regression. In this way the cluster analysis is ``supervised'' by the outcome variable. An alternate specification is that features in each cluster have the same compound symmetric normal distribution, and the conditional distribution of the outcome given the features has the same coefficient for each feature in a cluster.
License: GPL-2
Imports: mvtnorm, gtools
Collate: 'supcluster.R' 'concordmap.R' 'generate.cluster.data.R' 'tab1.R'
Packaged: 2015-05-18 17:29:07 UTC; das15
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-18 22:45:09

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New package smoof with initial version 1.0
Package: smoof
Type: Package
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.
Version: 1.0
Date: 2015-05-18
Authors@R: c(person("Jakob", "Bossek", email = "j.bossek@gmail.com", role = c("aut", "cre")))
URL: https://github.com/jakobbossek/smoof
BugReports: https://github.com/jakobbossek/smoof/issues
License: BSD_2_clause + file LICENSE
Depends: ParamHelpers (>= 1.3), BBmisc (>= 1.6), checkmate (>= 1.1)
Imports: ggplot2, RColorBrewer, plot3D, emoa
Suggests: testthat, rPython (>= 0.0-5)
LazyData: yes
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2015-05-18 13:56:16 UTC; jboss
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-18 22:44:12

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New package redist with initial version 1.0
Package: redist
Version: 1.0
Date: 2015-05-15
Title: Markov Chain Monte Carlo Methods for Redistricting Simulation
Author: Ben Fifield <bfifield@princeton.edu>, Alexander Tarr <atarr@princeton.edu>, Michael Higgins <mjh5@princeton.edu>, and Kosuke Imai <kimai@princeton.edu>
Maintainer: Ben Fifield <bfifield@princeton.edu>
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using a Markov Chain Monte Carlo algorithm. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. The algorithm also can be used in combination with efficient simulation methods such as simulated and parallel tempering algorithms. Tools for analysis such as inverse probability reweighting and plotting functionality are included. The package implements methods described in Fifield, Higgins, Imai and Tarr (2015) ``A New Automated Redistricting Simulator Using Markov Chain Monte Carlo,'' working paper available at <http://http://imai.princeton.edu/research/files/redist.pdf>.
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.0), spdep, sp, coda
LinkingTo: Rcpp, RcppArmadillo
License: GPL (>= 2)
SystemRequirements: gmp, libxml2
Packaged: 2015-05-18 01:14:02 UTC; benfifield
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-18 07:31:08

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Sun, 17 May 2015

New package rotationForest with initial version 0.1
Package: rotationForest
Type: Package
Title: Fit and Deploy Rotation Forest Models
Version: 0.1
Date: 2015-05-15
Imports: rpart
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@gmail.com>
Description: Fit and deploy rotation forest models ("Rodriguez, J.J., Kuncheva, L.I., 2006. Rotation forest: A new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28, 1619-1630") for binary classification. Rotation forest is an ensemble method where each base classifier (tree) is fit on the principal components of the variables of random partitions of the feature set.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-05-17 15:11:09 UTC; michelballings
Repository: CRAN
Date/Publication: 2015-05-18 01:14:15

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New package ssfa with initial version 1.0
Package: ssfa
Type: Package
Title: Spatial Stochastic Frontier Analysis
Version: 1.0
Date: 2015-05-15
Author: Elisa Fusco, Francesco Vidoli
Maintainer: Elisa Fusco <fusco_elisa@libero.it>
Description: Spatial Stochastic Frontier Analysis (SSFA) is an original method for controlling the spatial heterogeneity in Stochastic Frontier Analysis (SFA) models by splitting the inefficiency term into three terms: the first one related to spatial peculiarities of the territory in which each single unit operates, the second one related to the specific production features and the third one representing the error term.
Depends: Matrix, maxLik, spdep, sp
License: GPL-3
NeedsCompilation: no
Packaged: 2015-05-17 20:00:39 UTC; Elisa
Repository: CRAN
Date/Publication: 2015-05-18 00:52:19

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New package MInt with initial version 1.0.1
Package: MInt
Type: Package
Title: Learn Direct Interaction Networks
Version: 1.0.1
Date: 2015-05-17
Author: Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic
Maintainer: Surojit Biswas <surojitbiswas@g.harvard.edu>
Description: Learns direct microbe-microbe interaction networks using a Poisson multivariate-normal hierarchical model with an L1 penalized precision matrix. Optimization is carried out using an iterative conditional modes algorithm.
License: GPL-2
Depends: R (>= 3.1.2), glasso (>= 1.8), trust (>= 0.1-6), MASS (>= 7.3-35), testthat (>= 0.9.1)
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-05-17 15:32:02 UTC; sbiswas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-18 00:57:24

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New package Dark with initial version 0.9.4
Package: Dark
Type: Package
Title: The Analysis of Dark Adaptation Data
Version: 0.9.4
Date: 2015-05-17
Author: Dr Jeremiah MF Kelly
Maintainer: Dr Jeremiah MF Kelly <emkayoh@mac.com>
Description: The recovery of visual sensitivity in a dark environment is known as dark adaptation. In a clinical or research setting the recovery is typically measured after a dazzling flash of light and can be described by the Mahroo, Lamb and Pugh (MLP) model of dark adaptation. The functions in this package take dark adaptation data and use nonlinear regression to find the parameters of the model that 'best' describe the data. They do this by firstly, generating rapid initial objective estimates of data adaptation parameters, then a multi-start algorithm is used to reduce the possibility of a local minimum. There is also a bootstrap method to calculate parameter confidence intervals. The functions rely upon a 'dark' list or object. This object is created as the first step in the workflow and parts of the object are updated as it is processed.
License: GPL-3
LazyData: yes
URL: https://github.com/emkayoh/Dark, http://www.nihr.ac.uk
BugReports: https://github.com/emkayoh/Dark/issues
Suggests: knitr, rmarkdown,testthat
VignetteBuilder: knitr
Packaged: 2015-05-17 13:51:18 UTC; mqbxgjk2
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-18 00:56:57

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New package rchallenge with initial version 1.1
Package: rchallenge
Title: A Simple Datascience Challenge System
Version: 1.1
Authors@R: c(person("Adrien", "Todeschini", email = "adrien.todeschini@gmail.com",role=c("aut", "cre")), person("Robin", "Genuer", email = "robin.genuer@isped.u-bordeaux2.fr",role=c("ctb")))
Description: A simple datascience challenge system using R Markdown and Dropbox. It requires no network configuration, does not depend on external platforms like e.g. Kaggle and can be easily installed on a personal computer.
URL: http://adrtod.github.io/rchallenge
BugReports: https://github.com/adrtod/rchallenge/issues
Depends: R (>= 3.2.0)
Imports: rmarkdown (>= 0.5.1), knitr (>= 1.6)
SystemRequirements: pandoc (>= 1.12.3) - http://johnmacfarlane.net/pandoc
License: GPL-2
LazyData: true
NeedsCompilation: no
Packaged: 2015-05-16 11:45:43 UTC; adrien-alea
Author: Adrien Todeschini [aut, cre], Robin Genuer [ctb]
Maintainer: Adrien Todeschini <adrien.todeschini@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-17 16:38:17

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New package PoisBinOrdNonNor with initial version 1.0
Package: PoisBinOrdNonNor
Type: Package
Title: Generation of up to Four Different Types of Variables
Version: 1.0
Date: 2015-04-12
Author: Rachel Nordgren, Hakan Demirtas
Maintainer: Rachel Nordgren <rnordg2@uic.edu>
Description: Generation of a chosen number of count, binary, ordinal, and continuous (via Fleishman polynomials) random variables, with specified correlations and marginal properties.
License: GPL (>= 2)
Depends: Matrix, corpcor, MASS, GenOrd, BB
Suggests: moments
Packaged: 2015-05-17 02:00:48 UTC; Rachel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-17 09:53:54

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New package infuser with initial version 0.1
Package: infuser
Type: Package
Title: A Very Basic Templating Engine
Version: 0.1
Date: 2015-05-15
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Description: Replace parameters in strings and/or text files with specified values.
License: MIT + file LICENSE
LazyData: TRUE
Suggests: testthat
URL: https://github.com/bart6114/infuser/
BugReports: https://github.com/bart6114/infuser/issues
Packaged: 2015-05-16 18:50:04 UTC; bart
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-17 10:04:52

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Sat, 16 May 2015

New package TTmoment with initial version 1.0
Package: TTmoment
Type: Package
Title: Sampling and Calculating the First and Second Moments for the Doubly Truncated Multivariate t Distribution
Version: 1.0
Date: 2015-05-4
Author: Hsiu J. Ho, Tsung-I Lin, Wan-Lun Wang, Aldo M. Garay, Victor H. Lachos, and Mauricio Castro
Maintainer: Hsiu J. Ho <hsiujho@gmail.com>
Description: Computing the first two moments of the truncated multivariate t (TMVT) distribution under the double truncation. Appling the slice sampling algorithm to generate random variates from the TMVT distribution.
License: GPL-2
Depends: mvtnorm
Packaged: 2015-05-15 17:50:21 UTC; Peter
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-16 09:44:49

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New package simcausal with initial version 0.1
Package: simcausal
Type: Package
Title: Simulating Longitudinal Data with Causal Inference Applications
Version: 0.1
Date: 2015-05-14
Authors@R: c( person("Oleg", "Sofrygin", role=c("aut", "cre"), email="oleg.sofrygin@gmail.com"), person("Romain", "Neugebauer", role="aut", email="Romain.S.Neugebauer@kp.org"))
Description: A flexible tool for simulating complex longitudinal data using structural equations, with emphasis on problems in causal inference. Specify interventions and simulate from intervened data generating distributions. Define and evaluate treatment-specific means, the average treatment effects and coefficients from working marginal structural models. User interface designed to facilitate the conduct of transparent and reproducible simulation studies, and allows concise expression of complex functional dependencies for a large number of time-varying nodes.
Depends: R (>= 3.1.0)
Imports: data.table, reshape2
Suggests: ltmle, RUnit, knitr, igraph, ggplot2, Hmisc
License: GPL-2
Packaged: 2015-05-15 20:45:12 UTC; olegsofrygin
Author: Oleg Sofrygin [aut, cre], Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-16 09:52:34

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New package lawn with initial version 0.1.0
Package: lawn
Title: R Client for 'Turfjs' for 'Geospatial' Analysis
Description: R client for 'Turfjs' (http://turfjs.org/) for 'geospatial' analysis. The package revolves around using 'GeoJSON' data. Functions are included for creating 'GeoJSON' data objects, measuring aspects of 'GeoJSON', and combining, transforming, and creating random 'GeoJSON' data objects.
Type: Package
Version: 0.1.0
License: MIT + file LICENSE
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"), person("Jeff", "Hollister", role = "aut", email = "hollister.jeff@epa.gov") )
Additional_repositories: http://www.carlboettiger.info/drat
URL: https://github.com/ropensci/lawn
BugReports: http://www.github.com/ropensci/lawn/issues
LazyData: true
VignetteBuilder: knitr
Imports: V8, jsonlite, magrittr
Suggests: testthat, knitr, leaflet
Enhances: maps, geojsonio
NeedsCompilation: no
Packaged: 2015-05-16 01:29:56 UTC; sacmac
Author: Scott Chamberlain [aut, cre], Jeff Hollister [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-16 09:44:53

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Thu, 14 May 2015

New package FSInteract with initial version 0.1.1
Package: FSInteract
Type: Package
Title: Fast Searches for Interactions
Version: 0.1.1
Date: 2015-05-14
Author: Hyun Jik Kim, Rajen D. Shah
Maintainer: Rajen D. Shah <r.shah@statslab.cam.ac.uk>
Description: Performs fast detection of interactions in large-scale data using the method of random intersection trees introduced in ``Shah, R. D. and Meinshausen, N. (2014) Random Intersection Trees''. The algorithm finds potentially high-order interactions in high-dimensional binary two-class classification data, without requiring lower order interactions to be informative. The search is particularly fast when the matrices of predictors are sparse. It can also be used to perform market basket analysis when supplied with a single binary data matrix. Here it will find collections of columns which for many rows contain all 1's.
License: GPL-2
Depends: Rcpp (>= 0.11.2), Matrix (>= 1.0)
LinkingTo: Rcpp
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2015-05-14 15:01:12 UTC; rds37
Repository: CRAN
Date/Publication: 2015-05-15 00:04:47

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New package MCTM with initial version 1.0
Package: MCTM
Title: Markov Chains Transition Matrices
Description: Transition matrices (probabilities or counts) estimation for discrete Markov Chains of order n (1 <= n <= 5).
Version: 1.0
Author: Alessandro Bessi
Maintainer: Alessandro Bessi <alessandro.bessi@iusspavia.it>
Depends: R (>= 3.1.1)
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-14 08:27:05

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New package BinaryEPPM with initial version 1.0
Package: BinaryEPPM
Type: Package
Title: Mean and Variance Modeling of Binary Data
Version: 1.0
Imports: Formula, expm, numDeriv
Date: 2015-05-04
Author: David M Smith, Malcolm J Faddy
Maintainer: David M. Smith <david.m.smith@truvenhealth.com>
Description: Modeling under- and over-dispersed binary data using extended Poisson process models (EPPM).
License: GPL-2
NeedsCompilation: no
Packaged: 2015-05-05 00:19:15 UTC; U0117151
Repository: CRAN
Date/Publication: 2015-05-14 08:27:03

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Wed, 13 May 2015

New package acc with initial version 1.0.2
Package: acc
Type: Package
Title: Processes Accelerometer Data
Version: 1.0.2
Date: 2015-05-13
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>
Description: Processes accelerometer data, generates summaries and plots data.
Depends: R (>= 2.10)
License: GNU General Public License (>= 3)
Imports: zoo, PhysicalActivity, mhsmm, timeDate
Packaged: 2015-05-13 23:47:20 UTC; JS
Repository: CRAN
NeedsCompilation: no
Date/Publication: 2015-05-14 02:11:14

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New package stackoverflow with initial version 0.1.2
Package: stackoverflow
Type: Package
Title: Stack Overflow's Greatest Hits
Version: 0.1.2
Date: 2015-05-11
Author: Neal Fultz <nfultz@gmail.com> and the StackOverflow.com community
Maintainer: Neal Fultz <nfultz@gmail.com>
Description: Consists of helper functions collected from StackOverflow.com, a question and answer site for professional and enthusiast programmers.
License: CC BY-SA 4.0
URL: http://stackoverflow.com
NeedsCompilation: no
Packaged: 2015-05-13 16:36:13 UTC; njf
Repository: CRAN
Date/Publication: 2015-05-13 19:56:17

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New package perspectev with initial version 1.0
Package: perspectev
Type: Package
Title: Permutation of Species During Turnover Events
Version: 1.0
Date: 2015-05-02
Authors@R: c(person("Kenneth B.","Hoehn",role=c("aut","cre"),email="perspectev@gmail.com"), person("Glen A.","Sargeant",role="ctb",email="glen_sargeant@usgs.gov"))
Maintainer: Kenneth B. Hoehn <perspectev@gmail.com>
Depends: R (>= 2.10), ggplot2, foreach, ape, doParallel, parallel
Imports: mapproj, boot, sp
Description: Provides a robust framework for analyzing the extent to which differential survival with respect to higher level trait variation is reducible to lower level variation. In addition to its primary test, it also provides functions for simulation-based power analysis, reading in common data set formats, and visualizing results. Temporarily contains an edited version of function hr.mcp() from package 'wild1', written by Glen Sargeant.
License: GPL-3
NeedsCompilation: no
Packaged: 2015-05-13 17:14:30 UTC; ken
Author: Kenneth B. Hoehn [aut, cre], Glen A. Sargeant [ctb]
Repository: CRAN
Date/Publication: 2015-05-13 19:53:39

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New package MultiRR with initial version 1.0
Package: MultiRR
Type: Package
Title: Bias, Precision, and Power for Multi-Level Random Regressions
Version: 1.0
Date: 2015-05-11
Author: Yimen G. Araya-Ajoy
Maintainer: Yimen G. Araya-Ajoy <yimencr@gmail.com>
Depends:
Description: Calculates bias, precision, and power for multi-level random regressions. Random regressions are types of hierarchical models in which data are structured in groups and (regression) coefficients can vary by groups. Tools to estimate model performance are designed mostly for scenarios where (regression) coefficients vary at just one level. 'MultiRR' provides simulation and analytical tools (based on 'lme4') to study model performance for random regressions that vary at more than one level (multi-level random regressions), allowing researchers to determine optimal sampling designs.
License: GPL-2
Imports: MASS, lme4
NeedsCompilation: no
Packaged: 2015-05-13 09:13:13 UTC; yi
Repository: CRAN
Date/Publication: 2015-05-13 17:03:57

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New package cp4p with initial version 0.2
Package: cp4p
Type: Package
Title: Calibration Plot for Proteomics
Version: 0.2
Date: 2015-05-12
Author: Quentin Giai Gianetto, Florence Combes, Yohann Couté, Christophe Bruley, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
License: GPL-3
Depends: multtest, qvalue, limma, MESS
Encoding: UTF-8
Packaged: 2015-05-13 08:44:54 UTC; quentin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-13 17:01:01

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New package matchingR with initial version 1.0.1
Package: matchingR
Type: Package
Title: Gale-Shapley Algorithm in R and C++
Version: 1.0.1
Date: 2015-05-07
Author: Jan Tilly
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Description: Computes the Gale-Shapley Algorithm efficiently using Rcpp. Provides algorithms to compute the stable matching for the marriage problem and for the college-admissions problem, i.e. the matching of students to colleges.
License: GPL (>= 2)
Depends: Rcpp
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat
Packaged: 2015-05-13 01:12:32 UTC; jtilly
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-13 08:49:51

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Tue, 12 May 2015

New package smcfcs with initial version 1.0.0
Package: smcfcs
Title: Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification
Version: 1.0.0
Authors@R: person("Jonathan", "Bartlett", email = "jonathan.bartlett@lshtm.ac.uk", role = c("aut", "cre"))
URL: http://www.missingdata.org.uk, http://thestatsgeek.com
Description: Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.
Depends: R (>= 3.1.2)
License: GPL-3
LazyData: true
Imports: VGAM, MASS, survival
Suggests: knitr, mitools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-05-12 22:32:19 UTC; JWB-beast
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jonathan.bartlett@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2015-05-13 00:54:19

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New package odeintr with initial version 1.0
Package: odeintr
Type: Package
Title: C++ ODE Solvers Compiled on-Demand
Version: 1.0
Date: 2015-05-07
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt <tkeitt@gmail.com>
Description: Wraps the Boost odeint library for integration of differential equations.
URL: http://www.keittlab.org/
License: GPL (>= 2)
Imports: Rcpp (>= 0.10.0)
LinkingTo: Rcpp, BH
NeedsCompilation: yes
Packaged: 2015-05-07 19:36:55 UTC; tkeitt
Repository: CRAN
Date/Publication: 2015-05-12 17:25:34

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New package DSviaDRM with initial version 1.0
Package: DSviaDRM
Type: Package
Title: Exploring Disease Similarity in Terms of Dysfunctional Regulatory Mechanisms
Version: 1.0
Date: 2015-05-12
Author: Jing Yang
Maintainer: Jing Yang <yangjing@scbit.org>
Description: Elucidation of human disease similarities has emerged as an active research area, which is highly relevant to etiology, disease classification, and drug repositioning. This package was designed and implemented for identifying disease similarities. It contains five functions which are 'DCEA', 'DCpathway', 'DS', 'comDCGL' and 'comDCGLplot'. In 'DCEA' function, differentially co-expressed genes and differentially co-expressed links are extracted from disease vs. health samples. Then 'DCpathway' function assigns differential co-expression values of pathways to be the average differential co-expression value of their component genes. Then 'DS' employs partial correlation coefficient of pathways as the disease similarity for each disease pairs. And 'DS' contains a permutation process for evaluating the statistical significant of observed disease partial correlation coefficients. At last, 'comDCGL' and 'comDCGLplot' sort out shared differentially co-expressed genes and differentially co-expressed links with regulation information and visualize them.
Depends: R (>= 2.10)
Imports: igraph, ppcor
License: GPL (> 2)
LazyLoad: yes
LazyData: true
Repository: CRAN
Packaged: 2015-05-12 09:02:55 UTC; Administrator
NeedsCompilation: no
Date/Publication: 2015-05-12 11:45:13

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Mon, 11 May 2015

New package mglmn with initial version 0.0.2
Package: mglmn
Type: Package
Title: Model Averaging for Multivariate GLM with Null Models
Version: 0.0.2
Date: 2015-05-11
Author: Masatoshi Katabuchi and Akihiro Nakamura
Maintainer: Masatoshi Katabuchi <mattocci27@gmail.com>
Depends: R (>= 2.10), mvabund, snowfall
Description: Tools for univariate and multivariate generalized linear models with model averaging and null model technique.
License: GPL-2
Repository: CRAN
NeedsCompilation: no
Packaged: 2015-05-11 15:33:27 UTC; mattocci27
Date/Publication: 2015-05-11 18:42:41

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New package install.load with initial version 1.0.3
Package: install.load
Title: Check, Install and Load CRAN & USGS GRAN Packages
Version: 1.0.3
Depends: R (>= 3.0), compiler
Author: Original install_load function written by maloneypatr as a contribution to Stack Overflow on February 28 2014 (http://stackoverflow.com/questions/15155814/check-if-r-package-is-installed-then-load-library). Irucka Embry has enhanced the original function.
Maintainer: Irucka Embry <iembry@ecoccs.com>
Description: Checks the local R library(ies) to see if the required package(s) is/are installed or not. If the package(s) is/are not installed, then the package(s) will be installed along with the required dependency(ies). This function pulls source or binary packages from the Revolution Analytics CRAN mirror and/or the USGS GRAN Repository. Lastly, the chosen package(s) is/are loaded.
URL: https://gitlab.com/iembry/install.load
BugReports: https://gitlab.com/iembry/install.load/issues
License: CC BY-SA 4.0
LazyData: true
NeedsCompilation: no
Packaged: 2015-05-11 14:49:30 UTC; uoxyh
Repository: CRAN
Date/Publication: 2015-05-11 17:05:37

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New package rerddap with initial version 0.1.0
Package: rerddap
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes functions to search for datasets, get summary information on datasets, and fetch datasets, in either csv or 'netCDF' format. 'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Version: 0.1.0
Date: 2015-05-09
License: MIT + file LICENSE
Authors@R: c(person("Scott", "Chamberlain", role = c("aut","cre"), email = "myrmecocystus@gmail.com"))
URL: https://github.com/ropensci/rerddap
BugReports: http://www.github.com/ropensci/rerddap/issues
LazyData: true
VignetteBuilder: knitr
Imports: httr, dplyr, data.table, jsonlite, xml2, digest, ncdf
Suggests: roxygen2, knitr, testthat, ncdf4
Enhances: taxize
NeedsCompilation: no
Packaged: 2015-05-09 15:59:07 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-11 08:47:58

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New package plantecophys with initial version 0.6
Package: plantecophys
Type: Package
Title: Modelling and Analysis of Leaf Gas Exchange Data
Version: 0.6
Author: Remko Duursma
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Description: Coupled leaf gas exchange model, A-Ci curve simulation and fitting, leaf energy balance using Penman-Monteith, Cowan-Farquhar optimization, unit conversions.
License: GPL
LazyData: yes
NeedsCompilation: no
Packaged: 2015-05-10 23:40:19 UTC; 30022860
Repository: CRAN
Date/Publication: 2015-05-11 08:52:27

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Sun, 10 May 2015

New package csn with initial version 1.1.3
Package: csn
Type: Package
Title: Closed Skew-Normal Distribution
Version: 1.1.3
Date: 2015-05-09
Author: Dmitry Pavlyuk, Eugene Girtcius
Maintainer: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>
Depends: R (>= 2.2.0)
Imports: mvtnorm
Description: Provides functions for computing the density and the log-likelihood function of closed-skew normal variates, and for generating random vectors sampled from this distribution. See Gonzalez-Farias, G., Dominguez-Molina, J., and Gupta, A. (2004). The closed skew normal distribution, Skew-elliptical distributions and their applications: a journey beyond normality, Chapman and Hall/CRC, Boca Raton, FL, pp. 25-42.
License: GPL-2
Packaged: 2015-05-09 07:25:08 UTC; rforge
NeedsCompilation: no
Repository: CRAN
Repository/R-Forge/Project: csn
Repository/R-Forge/Revision: 10
Repository/R-Forge/DateTimeStamp: 2015-05-09 07:20:52
Date/Publication: 2015-05-10 23:27:41

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Sat, 09 May 2015

New package spTest with initial version 0.1.0
Package: spTest
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Date: 2015-05-08
Version: 0.1.0
Authors@R: person('Zachary', 'Weller', email = 'wellerz@stat.colostate.edu', role = c('aut', 'cre'))
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Suggests: mvtnorm, geoR, fields
Depends: R (>= 3.0.0)
License: GPL (>= 2)
LazyData: true
Packaged: 2015-05-09 15:25:15 UTC; ZachWeller
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-09 23:14:58

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New package solarius with initial version 0.2.3
Package: solarius
Type: Package
Title: An R Interface to SOLAR
Version: 0.2.3
Date: 2015-05-08
Authors@R: c( person("Andrey", "Ziyatdinov", email = "andrey.ziyatdinov@upc.edu", role = c("cre", "aut")), person("Helena", "Brunel", role = "aut"), person("Angel", "Martinez-Perez", role = "aut"), person("Alfonso", "Buil", role = "aut"), person("Alexandre", "Perera", role = "cph"), person("Jose Manuel", "Soria", role = "cph"))
Maintainer: Andrey Ziyatdinov <andrey.ziyatdinov@upc.edu>
Description: SOLAR is the standard software program to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. This package allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. See <http://solar.txbiomedgenetics.org/> for more information about SOLAR.
License: GPL (>= 3)
URL: https://github.com/ugcd/solarius
LazyData: false
Imports: methods, plyr (>= 1.8.1), ggplot2, data.table
Suggests: kinship2, scales, Matrix, gdata, doParallel, iterators, parallel, qqman
Collate: 'package.R' 'datasets.R' 'data.lib.R' 'support.lib.R' 'solar.lib.R' 'assoc.lib.R' 'classSolarAssoc.R' 'classSolarPolygenic.R' 'plot.lib.R' 'polygenic.lib.R' 'solarAssoc.R' 'solarPolygenic.R' 'files.lib.R' 'classSolarMultipoint.R' 'solarMultipoint.R' 'multipoint.lib.R' 'transforms.lib.R'
Packaged: 2015-05-08 21:04:39 UTC; andrey
Author: Andrey Ziyatdinov [cre, aut], Helena Brunel [aut], Angel Martinez-Perez [aut], Alfonso Buil [aut], Alexandre Perera [cph], Jose Manuel Soria [cph]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-09 06:20:42

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Fri, 08 May 2015

New package asVPC with initial version 1.0.2
Package: asVPC
Type: Package
Title: Average Shifted Visual Predictive Checks
Version: 1.0.2
Date: 2015-5-8
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Suggests: Hmisc
Imports: ggplot2,plyr
Description: The visual predictive checks are well-known method to validate the nonlinear mixed effect model, especially in pharmacometrics area. The average shifted visual predictive checks are the newly developed method of Visual predictive checks combined with the idea of the average shifted histogram.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-05-08 15:50:14 UTC; EKLee
Repository: CRAN
Date/Publication: 2015-05-08 20:02:08

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New package SpecHelpers with initial version 0.1.6
Package: SpecHelpers
Type: Package
Title: Spectroscopy Related Utilities
Version: 0.1.6
Date: 2015-05-08
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Description: Utility functions for spectroscopy. 1. Functions to simulate spectra for use in teaching or testing. 2. Functions to process files created by 'LoggerPro' and 'SpectraSuite' software.
License: GPL-3
Imports: gsubfn
URL: https://github.com/bryanhanson/SpecHelpers
ByteCompile: TRUE
BugReports: https://github.com/bryanhanson/SpecHelpers/issues
Depends: R (>= 3.0)
NeedsCompilation: no
Packaged: 2015-05-08 14:18:14 UTC; bryanhanson
Repository: CRAN
Date/Publication: 2015-05-08 16:52:18

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New package PPtreeViz with initial version 1.0.1
Package: PPtreeViz
Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using LDA, Lr or PDA projection pursuit index.
Version: 1.0.1
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Date: 2015-5-8
Depends: R (>= 2.10),gridExtra,ggplot2,grid
Suggests: MASS (>= 3.1-20)
Imports: Rcpp, reshape2
LinkingTo: Rcpp, RcppArmadillo
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2015-05-08 12:20:20 UTC; EKLee
Repository: CRAN
Date/Publication: 2015-05-08 16:52:15

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New package MultiJoin with initial version 0.1
Package: MultiJoin
Type: Package
Title: Enables Efficient Joining of Data File on Common Fields using the Unix Utility Join
Version: 0.1
Date: 2015-05-07
Depends: R (>= 2.10), graphics, stats
Author: "Markus Loecher, Berlin School of Economics and Law (BSEL)" <markus.loecher@gmail.com>
Maintainer: "Markus Loecher" <markus.loecher@gmail.com>
Description: Wrapper around the Unix join facility which is more efficient than the built-in R routine merge(). The package enables the joining of multiple files on disk at once. The files can be compressed and various filters can be deployed before joining. Compiles only under Unix.
License: GPL
LazyLoad: yes
Packaged: 2015-05-08 10:22:43 UTC; loecherm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-08 16:52:14

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New package sgd with initial version 0.1
Package: sgd
Type: Package
Title: Stochastic Gradient Descent for Scalable Estimation
Version: 0.1
Authors@R: c( person("Dustin", "Tran", email = "dtran@g.harvard.edu", role = c("aut", "cre")), person("Tian", "Lian", role = "aut"), person("Panos", "Toulis", role = "aut"), person("Ye", "Kuang", role = "ctb"), person("Edoardo", "Airoldi", role = "ctb") )
Maintainer: Dustin Tran <dtran@g.harvard.edu>
Description: A fast and flexible set of tools for large scale inference. It features many different stochastic gradient methods, built-in models, visualization tools, automated hyperparameter tuning, model checking, interval estimation, and convergence diagnostics.
URL: https://github.com/airoldilab/sgd
BugReports: https://github.com/airoldilab/sgd/issues
License: GPL-2
Imports: Rcpp (>= 0.11.3), MASS
LinkingTo: Rcpp, RcppArmadillo, BH
Packaged: 2015-05-08 03:07:56 UTC; dvt
Author: Dustin Tran [aut, cre], Tian Lian [aut], Panos Toulis [aut], Ye Kuang [ctb], Edoardo Airoldi [ctb]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-08 11:45:39

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New package ddeploy with initial version 1.0.2
Package: ddeploy
Type: Package
Title: Wrapper for the Duke Deploy REST API
Version: 1.0.2
Date: 2015-05-04
Author: person("Niall", "McGearailt", role = c("aut", "cre"),email = "niall@dukeanalytics.com")
Maintainer: Niall McGearailt <niall@dukeanalytics.com>
Description: A wrapper for the Duke Analytics model deployment API. See <http://www.dukeanalytics.com/products/dukedeployR.php> for more details.
License: GPL
Depends: R (>= 3.0.0)
Imports: httr, jsonlite
Packaged: 2015-05-07 21:33:23 UTC; nf
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-08 11:45:18

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New package brms with initial version 0.1.0
Package: brms
Type: Package
Title: Bayesian Regression Models using Stan
Version: 0.1.0
Date: 2015-05-07
Authors@R: person("Paul-Christian", "Buerkner", email = "paul.buerkner@gmail.com", role = c("aut", "cre"))
Depends: R (>= 3.1.0), ggplot2 (>= 1.0.1), Rcpp (>= 0.11.5)
Imports: methods, parallel (>= 3.1.3), coda (>= 0.17-1), ggmcmc (>= 0.6), gridExtra (>= 0.9.1)
Suggests: rstan (>= 2.6.0), R2jags (>= 0.05-03), testthat (>= 0.9.1)
Description: Write and fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
LazyData: true
NeedsCompilation: no
License: GPL (>= 2)
Additional_repositories: http://rstan.org/repo
Packaged: 2015-05-08 08:19:42 UTC; Paul
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Repository: CRAN
Date/Publication: 2015-05-08 11:47:48

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New package ApacheLogProcessor with initial version 0.1
Package: ApacheLogProcessor
Type: Package
Title: Process the Apache Web Server Log Combined Files
Version: 0.1
Date: 2015-05-06
Author: Diogo Silveira Mendonca
Maintainer: Diogo Silveira Mendonca <diogosmendonca@gmail.com>
Description: Provides a function to process Apache Log Combined files. The main functionality is to extract data from log files to data frames.
License: LGPL-3
Imports: foreach, parallel, doParallel
NeedsCompilation: no
Packaged: 2015-05-07 23:40:44 UTC; diogo
Repository: CRAN
Date/Publication: 2015-05-08 11:45:15

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Thu, 07 May 2015

New package cranlogs with initial version 2.0.0
Package: cranlogs
Title: Download Logs from the RStudio CRAN Mirror
Version: 2.0.0
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Author: Gabor Csardi [aut, cre]
Description: API to the database of CRAN package downloads from the RStudio CRAN mirror. The database itself is at http://cranlogs.r-pkg.org, see https://github.com/metacran/cranlogs.app for the raw API.
License: MIT + file LICENSE
URL: https://github.com/metacran/cranlogs
BugReports: https://github.com/metacran/cranlogs/issues
Imports: httr, jsonlite
NeedsCompilation: no
Packaged: 2015-05-07 18:08:40 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2015-05-07 22:30:29

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New package alphaOutlier with initial version 1.0.0
Package: alphaOutlier
Type: Package
Title: Obtain Alpha-Outlier Regions for Well-Known Probability Distributions
Version: 1.0.0
Date: 2015-05-07
Author: Andre Rehage, Sonja Kuhnt
Maintainer: Andre Rehage <rehage@statistik.tu-dortmund.de>
Description: Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, doi: 10.1080/01621459.1993.10476339 for details.
License: GPL-3
Depends: Rsolnp, nleqslv, quantreg
NeedsCompilation: no
Packaged: 2015-05-07 11:04:08 UTC; rehage
Repository: CRAN
Date/Publication: 2015-05-07 18:01:58

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New package QFRM with initial version 1.0
Package: QFRM
Type: Package
Title: Pricing of Vanilla and Exotic Option Contracts
Version: 1.0
Date: 2015-05-03
Maintainer: Oleg Melnikov <XisReal@gmail.com>
Authors@R: c( person("Oleg", "Melnikov", role = c("aut", "cre"), email = "XisReal@gmail.com"), person("Max", "Lee", role = "ctb", email = "max.lee@rice.edu"), person("Robert", "Abramov", role = "ctb", email = "rha1@rice.edu"), person("Richard", "Huang", role = "ctb", email = "richard.b.huang@rice.edu"), person("Liu", "Tong", role = "ctb", email = "tong.liu@rice.edu"), person("Jake", "Kornblau", role = "ctb", email = "jake.a.kornblau@rice.edu"), person("Xinnan", "Lu", role = "ctb", email = "xinnan.lu@rice.edu"), person("Kiryl", "Novikau", role = "ctb", email = "kiryl.novikau@rice.edu"), person("Tongyue", "Luo", role = "ctb", email = "tongyue.luo@rice.edu"), person("Le", "You", role = "ctb", email = "le.you@rice.edu"), person("Jin", "Chen", role = "ctb", email = "jin.chen@rice.edu"), person("Chengwei", "Ge", role = "ctb", email = "chengwei.ge@rice.edu"), person("Jiayao", "Huang", role = "ctb", email = "jiayao.huang@rice.edu") )
Description: Option pricing (financial derivatives) techniques mainly following textbook 'Options, Futures and Other Derivatives', 9ed by John C.Hull, 2014. Prentice Hall. Implementations are via binomial tree option model (BOPM), Black-Scholes model, Monte Carlo simulations, etc. This package is a result of Quantitative Financial Risk Management course (STAT 449 and STAT 649) at Rice University, Houston, TX, USA, taught by Oleg Melnikov, statistics PhD student, as of Spring 2015.
Repository: CRAN
License: GPL (>= 2)
URL: http://Oleg.Rice.edu
NeedsCompilation: no
Depends: R (>= 2.14.0)
LazyLoad: yes
LazyData: yes
Packaged: 2015-05-07 04:28:57 UTC; Oleggio
Author: Oleg Melnikov [aut, cre], Max Lee [ctb], Robert Abramov [ctb], Richard Huang [ctb], Liu Tong [ctb], Jake Kornblau [ctb], Xinnan Lu [ctb], Kiryl Novikau [ctb], Tongyue Luo [ctb], Le You [ctb], Jin Chen [ctb], Chengwei Ge [ctb], Jiayao Huang [ctb]
Date/Publication: 2015-05-07 07:48:37

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New package loopr with initial version 1.0.0
Package: loopr
Type: Package
Title: Uses an Archive to Amend Previous Stages of a Pipe using Current Output
Version: 1.0.0
Date: 2015-05-07
Author: Brandon Taylor
Maintainer: Brandon Taylor <Brandon.Taylor221@gmail.com>
Description: Remedies a common problem in piping: not having access to intermediate outputs of the pipe. Within a "loop", a piping intermediate is stored in a stack archive, data is processed, and then both the stored intermediate and the current output are reintegrated using an "ending" function. Two special ending functions are provided: amend and insert. However, any ending function can be specified, including merge functions, join functions, setNames(), etc. This framework allows the following workflow: focus on a particular aspect or section of a dataset, conduct specific operations, and then reintegrate changes into the whole.
Depends: R (>= 3.1.3)
Imports: plyr (>= 1.8.1), dplyr (>= 0.4.1), magrittr (>= 1.5), lazyeval (>= 0.1.10), R6 (>= 2.0.1)
License: MIT + file LICENSE
LazyData: true
Suggests: knitr (>= 1.9)
VignetteBuilder: knitr
Packaged: 2015-05-07 04:40:30 UTC; haldane
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-07 07:48:38

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Wed, 06 May 2015

New package dynRB with initial version 0.1
Package: dynRB
Type: Package
Title: Dynamic Range Boxes
Version: 0.1
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at> and Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
License: GPL-2
Packaged: 2015-05-06 14:09:09 UTC; b1015748
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-06 17:04:44

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New package SpatialPosition with initial version 0.9
Package: SpatialPosition
Title: Spatial Position Models
Version: 0.9
Authors@R: c( person("Timothee", "Giraud", email = "timothee.giraud@ums-riate.fr", role = c("cre","aut")), person("Hadrien", "Commenges", email = "hcommenges@parisgeo.cnrs.fr", role = c("aut")), person("Joel", "Boulier", email = "joel.boulier@univ-paris1.fr", role = c("ctb")))
Description: Computes spatial position models: Stewart potentials, Reilly catchment areas, Huff catchment areas.
Depends: R (>= 3.0.0), raster
License: GPL-3
LazyData: true
Imports: sp
Suggests: rgeos, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-05-06 09:23:23 UTC; tg
Author: Timothee Giraud [cre, aut], Hadrien Commenges [aut], Joel Boulier [ctb]
Maintainer: Timothee Giraud <timothee.giraud@ums-riate.fr>
Repository: CRAN
Date/Publication: 2015-05-06 14:46:24

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New package Scale with initial version 1.0.4
Package: Scale
Type: Package
Title: Likert Type Questionnaire Item Analysis
Version: 1.0.4
Date: 2015-05-05
Author: Nikolaos Giallousis
Maintainer: Nikolaos Giallousis <psierevn@gmail.com>
Description: Provides the Scale class and corresponding functions, in order to facilitate data input for scale construction. Reverse items and alternative orders of administration are dealt with by the program. Computes reliability statistics, confirmatory, single factor loadings. It suggests item deletions and produces basic text output in English, for incorporation in reports. Returns list objects of all relevant functions from other packages (see Depends).
License: GPL-2
Depends: psych, Hmisc, MASS
URL:
Suggests:
LazyData: true
Packaged: 2015-05-05 22:10:17 UTC; N31k
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-06 14:46:23

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New package riceware with initial version 0.2
Package: riceware
Title: A Diceware Passphrase Implementation
Version: 0.2
Authors@R: c( person("Francois", "Michonneau", role=c("aut", "cre"), email="francois.michonneau@gmail.com"), person("Arnold G.", "Reinhold", role=c("cph")) )
Description: The Diceware method can be used to generate strong passphrases. In short, you roll a 6-faced dice 5 times in a row, the number obtained is matched against a dictionary of easily remembered word. By combining together 7 words thus generated, you obtain a password that is relatively easy to remember, but would take several millions years (on average) for a powerful computer to guess.
Depends: R (>= 3.1.3)
Imports: random
License: MIT + file LICENSE
LazyData: true
Suggests: testthat
Packaged: 2015-05-05 21:57:27 UTC; francois
Author: Francois Michonneau [aut, cre], Arnold G. Reinhold [cph]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-06 14:46:34

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Tue, 05 May 2015

New package rankdist with initial version 0.3.1
Package: rankdist
Type: Package
Title: Distance Based Ranking Models
Version: 0.3.1
Date: 2015-05-01
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Description: Implements distance based probability models for ranking data. The supported distance metrics include Kendall distance and Weighted Kendall distance. Mixture models are also supported.
License: GPL (>= 2)
Depends: R (>= 2.10)
Imports: Rcpp (>= 0.11.4), hash, optimx, methods
LinkingTo: Rcpp
LazyData: true
Suggests: testthat
Packaged: 2015-05-05 15:45:09 UTC; Steven
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-05 23:29:27

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New package RPEnsemble with initial version 0.1
Package: RPEnsemble
Type: Package
Title: Random Projection Ensemble Classification
Version: 0.1
Date: 2015-05-05
Author: Timothy I. Cannings and Richard J. Samworth
Maintainer: Timothy I. Cannings <t.cannings@statslab.cam.ac.uk>
Description: Implements the methodology of "Cannings, T. I. and Samworth, R. J. (2015) Random projection ensemble classification. http://arxiv.org/abs/1504.04595". The random projection ensemble classifier is a very general method for classification of high-dimensional data, based on careful combination of the results of applying an arbitrary base classifier to random projections of the feature vectors into a lower-dimensional space. The random projections are divided into non-overlapping blocks, and within each block the projection yielding the smallest estimate of the test error is selected. The random projection ensemble classifier then aggregates the results of applying the base classifier on the selected projections, with a data-driven voting threshold to determine the final assignment.
Depends: R (>= 3.0.0), MASS
Imports: class, parallel, stats
License: GPL-3
LazyLoad: Yes
URL: http://arxiv.org/abs/1504.04595, http://www.statslab.cam.ac.uk/~tc325/
NeedsCompilation: no
Packaged: 2015-05-05 08:35:40 UTC; tc325
Repository: CRAN
Date/Publication: 2015-05-05 17:32:05

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New package reGenotyper with initial version 1.2.0
Package: reGenotyper
Type: Package
Title: Detecting Mislabeled Samples in Genetic Data
Version: 1.2.0
Date: 2015-05-04
Author: Yang Li <yang.li@rug.nl>
Maintainer: Yang Li <yang.li@rug.nl>
Description: Detecting mislabeled samples in genetic data.
Depends: R (>= 3.0.1), gplots, zoo, methods, MatrixEQTL
License: GPL
NeedsCompilation: no
Packaged: 2015-05-04 14:18:24 UTC; Konrad
Repository: CRAN
Date/Publication: 2015-05-05 16:14:49

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New package NNTbiomarker with initial version 0.28
Package: NNTbiomarker
Type: Package
Title: Calculate Design Parameters for Biomarker Validation Studies
Version: 0.28
Date: 2015-05-05
Author: Roger Day
Maintainer: Roger Day <day01@pitt.edu>
Description: Helps a clinical trial team discuss the clinical goals of a well-defined biomarker with a diagnostic, staging, prognostic, or predictive purpose. From this discussion will come a statistical plan for a (non-randomized) validation trial. Both prospective and retrospective trials are supported. In a specific focused discussion, investigators should determine the range of "discomfort" for the NNT, number needed to treat. The meaning of the discomfort range, [NNTlower, NNTupper], is that within this range most physicians would feel discomfort either in treating or withholding treatment. A pair of NNT values bracketing that range, NNTpos and NNTneg, become the targets of the study's design. If the trial can demonstrate that a positive biomarker test yields an NNT less than NNTlower, and that a negative biomarker test yields an NNT less than NNTlower, then the biomarker may be useful for patients. A highlight of the package is visualization of a "contra-Bayes" theorem, which produces criteria for retrospective case-controls studies.
License: GPL-3
Imports: shiny, xtable, stringr
Collate: aaa.R ifVerboseCat.R sesp-pv-NNT.R achievable.se.sp.R binom.confint.R NNTintervals.R run.R
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-05-05 04:07:44 UTC; Roger
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-05 16:14:37

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New package fbroc with initial version 0.1.0
Package: fbroc
Type: Package
Title: Fast Algorithms to Bootstrap ROC Curves
Version: 0.1.0
Date: 2015-04-29
Authors@R: c(person("Erik", "Peter", email = "jerikpeter@googlemail.com", role = c("aut", "cre")))
Description: Implements a very fast C++ algorithm to quickly bootstrap ROC Curves and derived performance metrics (e.g. AUC). You can also plot the results and calculate confidence intervals. Currently the calculation of 100000 bootstrap replicates for 500 observations takes about one second.
License: GPL-2
URL: http://github.com/erikpeter/fbroc
BugReports: http://github.com/erikpeter/fbroc/issues
Depends: R (>= 3.1.0), ggplot2
Imports: Rcpp
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2015-05-05 12:52:17 UTC; Erik
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Repository: CRAN
Date/Publication: 2015-05-05 16:14:44

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New package abc.data with initial version 1.0
Package: abc.data
Type: Package
Title: Data Only: Tools for Approximate Bayesian Computation (ABC)
Version: 1.0
Date: 2015-05-04
Authors@R: c( person("Csillery", "Katalin", role = "aut", email="kati.csillery@gmail.com"), person("Lemaire", "Louisiane", role = "aut"), person("Francois", "Olivier", role = "aut"), person("Blum", "Michael", email = "michael.blum@imag.fr", role = c("aut", "cre")))
Depends: R (>= 2.10)
Description: Contains data which are used by functions of the 'abc' package.
Repository: CRAN
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2015-05-05 09:25:25 UTC; mblum
Author: Csillery Katalin [aut], Lemaire Louisiane [aut], Francois Olivier [aut], Blum Michael [aut, cre]
Maintainer: Blum Michael <michael.blum@imag.fr>
Date/Publication: 2015-05-05 11:34:13

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New package hiertest with initial version 1.1
Package: hiertest
Title: Convex Hierarchical Testing of Interactions
Version: 1.1
Author: Jacob Bien, Noah Simon, and Rob Tibshirani
Maintainer: Jacob Bien <jbien@cornell.edu>
Description: Implementation of the convex hierarchical testing (CHT) procedure introduced in Bien, Simon, and Tibshirani (2015) Convex Hierarchical Testing of Interactions. Annals of Applied Statistics. Vol. 9, No. 1, 27-42.
Depends: R (>= 3.0.2)
License: GPL-3
LazyData: true
Packaged: 2015-05-05 04:57:41 UTC; jbien
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-05 07:53:06

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New package optifunset with initial version 1.0
Package: optifunset
Type: Package
Title: Set Options if Unset
Version: 1.0
Date: 2015-05-05
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton <n.hamilton@unsw.edu.au>
Description: A single function 'options.ifunset(...)' is contained herewith, which allows the user to set a global option ONLY if it is not already set. By this token, for package maintainers this function can be used in preference to the standard 'options(...)' function, making provision for THEIR end user to place 'options(...)' directives within their '.Rprofile' file, which will not be overridden at the point when a package is loaded.
License: GPL-2
Collate: 'onLoad.R' 'options-ifunset.R'
Packaged: 2015-05-05 04:22:25 UTC; nick
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-05 06:43:05

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New package manifestoR with initial version 0.9-12
Package: manifestoR
Title: Access and Process Data and Documents of the Manifesto Project
Date: 2015-05-04
Version: 0.9-12
Authors@R: c(person("Jirka", "Lewandowski", role = c("aut", "cre"), email = "jirka.lewandowski@wzb.eu"), person("Nicolas", "Merz", role = c("aut"), email = "nicolas.merz@wzb.eu"), person("Sven", "Regel", role = c("ctb"), email = "sven.regel@wzb.eu"), person("Pola", "Lehmann", role = c("ctb"), email = "pola.lehmann@wzb.eu"))
Description: Provides access to coded election programmes from the Manifesto Corpus and to the Manifesto Project's Main Dataset. The Manifesto Project (https://manifesto-project.wzb.eu) collects and analyses election programmes across time and space to measure the political preferences of parties. The Manifesto Corpus contains the collected and annotated election programmes in the Corpus format of the package 'tm' to enable easy use of text processing and text mining functionality. Specific functions for scaling of coded political texts are included.
Depends: R (>= 3.1.0), NLP (>= 0.1-3), tm (>= 0.6), dplyr (>= 0.4.1)
Imports: utils, httr (>= 0.3), jsonlite (>= 0.9.12), functional (>= 0.6)
Suggests: knitr, rmarkdown, testthat, R.rsp
VignetteBuilder: R.rsp
Collate: manifestoR-package.r globals.R cache.R db_api.R corpus.R manifesto.R codes.R scaling_general.R scaling_rile.R scaling_functions.R scaling_bootstrap.R renaming.R
License: GPL (>= 3)
URL: https://github.com/ManifestoProject/manifestoR, https://manifesto-project.wzb.eu/
BugReports: https://github.com/ManifestoProject/manifestoR/issues
LazyData: true
Packaged: 2015-05-04 14:58:04 UTC; manifesto
Author: Jirka Lewandowski [aut, cre], Nicolas Merz [aut], Sven Regel [ctb], Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-05 06:18:46

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New package LocFDRPois with initial version 1.0.0
Package: LocFDRPois
Title: Functions for Performing Local FDR Estimation when Null and Alternative are Poisson
Version: 1.0.0
Authors@R: person("Kris", "Sankaran", , "kriss1@stanford.edu", role = c("aut", "cre"))
Description: The main idea of the Local FDR algorithm is to estimate both proportion of null observations and the ratio of null and alternative densities. In the case that there are many null observations, this can be done reliably, through maximum likelihood or generalized linear models. This package implements this in the case that the null and alternative densities are Poisson.
Depends: R (>= 3.1.2)
Imports: dplyr, ggplot2
License: GPL-2
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-05-05 04:23:44 UTC; krissankaran
Author: Kris Sankaran [aut, cre]
Maintainer: Kris Sankaran <kriss1@stanford.edu>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-05 06:43:01

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New package biorxivr with initial version 0.1.0
Package: biorxivr
Type: Package
Title: Search and Download Papers from the bioRxiv Preprint Server
Version: 0.1.0
Date: 2015-04-15
Authors@R: c(person("Edmund", "Hart", role = c("aut","cre"), email = "edmund.m.hart@gmail.com"))
Maintainer: Edmund Hart <edmund.m.hart@gmail.com>
LazyLoad: yes
LazyData: yes
Description: The bioRxiv preprint server (http://www.biorxiv.org) is a website where scientists can post preprints of scholarly texts in biology. Users can search and download PDFs in bulk from the preprint server. The text of abstracts are stored as raw text within R, and PDFs can easily be saved and imported for text mining with packages such as 'tm'.
License: MIT + file LICENSE
Depends: XML
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-04-23 15:58:57 UTC; edmundhart
Author: Edmund Hart [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-05 06:18:45

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Mon, 04 May 2015

New package RANN.L1 with initial version 2.5
Encoding: UTF-8
Package: RANN.L1
Title: Fast Nearest Neighbour Search (Wraps ANN Library) Using L1 Metric
Version: 2.5
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis, Kirill Müller
Copyright: ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details.
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L1 (Manhattan, taxicab) metric. Please see package 'RANN' for the same functionality using the L2 (Euclidean) metric.
Maintainer: Kirill Müller
License: GPL (>= 3)
URL: https://github.com/jefferis/RANN/tree/master-L1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2015-05-04 08:20:21 UTC; muelleki
Repository: CRAN
Date/Publication: 2015-05-04 11:54:30

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New package clustering.sc.dp with initial version 1.0
Package: clustering.sc.dp
Type: Package
Title: Optimal Distance-Based Clustering for Multidimensional Data with Sequential Constraint
Version: 1.0
Date: 2015-04-28
Authors@R: c(person("Tibor", "Szkaliczki", role = c("aut", "cre"), email = "szkaliczki.tibor@sztaki.mta.hu"), person("J.", "Song", role = "ctb", email = "joemsong@cs.nmsu.edu"))
Author: Tibor Szkaliczki [aut, cre], J. Song [ctb]
Maintainer: Tibor Szkaliczki
Depends: R (>= 2.10.0)
Description: A dynamic programming algorithm for optimal clustering multidimensional data with sequential constraint. The algorithm minimizes the sum of squares of within-cluster distances. The sequential constraint allows only subsequent items of the input data to form a cluster. The sequential constraint is typically required in clustering data streams or items with time stamps such as video frames, GPS signals of a vehicle, movement data of a person, e-pen data, etc. The algorithm represents an extension of Ckmeans.1d.dp to multiple dimensional spaces. Similarly to the one-dimensional case, the algorithm guarantees optimality and repeatability of clustering. Method clustering.sc.dp can find the optimal clustering if the number of clusters is known. Otherwise, methods findwithinss.sc.dp and backtracking.sc.dp can be used.
License: LGPL (>= 3)
NeedsCompilation: yes
Packaged: 2015-05-04 06:24:46 UTC; Asus
Repository: CRAN
Date/Publication: 2015-05-04 09:27:25

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New package Rlinkedin with initial version 0.1
Package: Rlinkedin
Version: 0.1
Title: Access to the LinkedIn API via R
Description: A series of functions that allow users to access the LinkedIn API to get information about connections, search for people and jobs, share updates with their network, and create group discussions. For more information about using the API please visit https://developer.linkedin.com/.
Author: Michael Piccirilli
Maintainer: Michael Piccirilli
Depends: R (>= 2.12.0), httr, XML, httpuv
License: GPL-2
LazyData: true
URL: https://github.com/mpiccirilli/Rlinkedin
Packaged: 2015-05-04 04:10:10 UTC; mikepicc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-04 07:41:06

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Sun, 03 May 2015

New package ivmodel with initial version 1.0
Package: ivmodel
Type: Package
Title: Statistical Inference and Diagnostics for Instrumental Variables Model
Version: 1.0
Date: 2015-04-30
Author: Yang Jiang, Hyunseung Kang, and Dylan Small
Maintainer: Hyunseung Kang
Description: Contains functions for carrying out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics.
Depends: Matrix
License: GPL-2
Packaged: 2015-05-03 17:56:46 UTC; khyuns
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-04 01:31:33

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New package QCAfalsePositive with initial version 0.11
Package: QCAfalsePositive
Title: Tests for Type I Error in Qualitative Comparative Analysis (QCA)
Version: 0.11
Author: Bear Braumoeller
Maintainer: Bear Braumoeller
Description: Implements tests for Type I error in Qualitative Comparative Analysis (QCA) that take into account the multiple hypothesis tests inherent in the procedure. Tests can be carried out on three variants of QCA: crisp-set QCA (csQCA), multi-value QCA (mvQCA) and fuzzy-set QCA (fsQCA). For fsQCA, the fsQCApermTest() command implements a permutation test that provides 95% confidence intervals for the number of counterexamples and degree of consistency, respectively. The distributions of permuted values can be plotted against the observed values. For csQCA and mvQCA, simple binomial tests are implemented in csQCAbinTest() and mvQCAbinTest(), respectively.
Depends: R (>= 3.2.0)
License: GPL-3
LazyData: true
Note: For details and derivation, see Braumoeller, Bear F. "Guarding Against False Positives in Qualitative Comparative Analysis." Forthcoming, Political Analysis.
NeedsCompilation: no
Packaged: 2015-05-02 19:18:50 UTC; bfbraum
Repository: CRAN
Date/Publication: 2015-05-03 07:07:31

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New package neotoma with initial version 1.2-0
Package: neotoma
Type: Package
Title: Access to the Neotoma Paleoecological Database Through R
Version: 1.2-0
Date: 2015-05-01
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Authors@R: c(person(given = c("Simon", "J."), family = "Goring", role = c("aut", "cre"), email = "goring@wisc.edu"), person(given = c("Gavin", "L."), family = "Simpson", role = "aut"), person(given = c("Jeremiah", "P."), family = "Marsicek", role = "ctb"), person(given = "Karthik", family = "Ram", role = "aut"), person(given = "Luke", family = "Sosalla", role = "ctb"))
Maintainer: Simon J. Goring
Description: Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (http://api.neotomadb.org/). The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.
License: MIT + file LICENSE
URL: https://github.com/ropensci/neotoma
BugReports: https://github.com/ropensci/neotoma/issues
Depends: R (>= 2.10)
Imports: RJSONIO, RCurl (>= 1.6), plyr, reshape2
Suggests: testthat, knitr
NeedsCompilation: no
Packaged: 2015-05-02 15:11:25 UTC; Simon Goring
Repository: CRAN
Date/Publication: 2015-05-03 07:07:39

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New package fheatmap with initial version 1.0.0
Package: fheatmap
Type: Package
Title: Draw Heatmaps with Colored Dendogram
Version: 1.0.0
Date: 2015-05-02
Author: Vaishali Tumulu and Sivasish Sindiri
Maintainer: Sivasish Sindiri
Depends: R (>= 3.0)
Description: R function to plot high quality, elegant heatmap using 'ggplot2' graphics . Some of the important features of this package are, coloring of row/column side tree with respect to the number of user defined cuts in the cluster, add annotations to both columns and rows, option to input annotation palette for tree and column annotations and multiple parameters to modify aesthetics (style, color, font) of texts in the plot.
License: GPL-3
LazyData: true
Imports: grid, RColorBrewer , gdata, ggplot2, reshape2, gplots
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-05-02 17:21:10 UTC; sivasishsindiri
Date/Publication: 2015-05-03 07:07:38

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New package EW with initial version 1.1
Package: EW
Type: Package
Title: Edgeworth Expansion
Version: 1.1
Date: 2015-04-28
Author: H.R.Law
Maintainer: H.R.Law <4islands@gmail.com>
Description: Edgeworth Expansion calculation.
License: GPL
NeedsCompilation: no
Packaged: 2015-04-28 05:52:09 UTC; abc
Repository: CRAN
Date/Publication: 2015-05-03 07:07:26

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Sat, 02 May 2015

New package tidyjson with initial version 0.2.1
Package: tidyjson
Title: A Grammar for Turning 'JSON' into Tidy Tables
Version: 0.2.1
Author: Jeremy Stanley
Maintainer: Jeremy Stanley
Description: An easy and consistent way to turn 'JSON' into tidy data frames that are natural to work with in 'dplyr', 'ggplot2' and other tools.
Depends: R (>= 3.1.0)
Imports: assertthat, jsonlite, dplyr
URL: https://github.com/sailthru/tidyjson
License: MIT + file LICENSE
LazyData: true
Suggests: knitr, testthat, ggplot2, magrittr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-04-28 10:24:05 UTC; jeremystanley
Repository: CRAN
Date/Publication: 2015-05-02 23:54:28

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New package survJamda.data with initial version 1.0.2
Package: survJamda.data
Type: Package
Title: Data for Package 'survJambda'
Version: 1.0.2
Date: 2015-05-01
Author: Haleh Yasrebi
Maintainer: Haleh Yasrebi
Description: Three breast cancer gene expression data sets that can be used for package 'survJamda'. This package contains the gene expression and phenotype data of GSE1992, GSE3143 and GSE4335.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2015-05-02 13:53:17 UTC; hyasrebi
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-02 16:31:07

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New package survJamda with initial version 1.1.3
Package: survJamda
Type: Package
Title: Survival Prediction by Joint Analysis of Microarray Gene Expression Data
Version: 1.1.3
Date: 2015-05-01
Author: Haleh Yasrebi
Maintainer: Haleh Yasrebi
Description: Microarray gene expression data can be analyzed individually or jointly using merging methods or meta-analysis to predict patients' survival and risk assessment.
Depends: survival, survivalROC,ecodist,survcomp,survJamda.data
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2015-05-01 10:03:58 UTC; yasrebih
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-02 16:31:04

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New package muir with initial version 0.1.0
Package: muir
Type: Package
Title: Exploring Data with Tree Data Structures
Version: 0.1.0
Authors@R: person("Justin", "Alford", , "justin.alford@gmail.com", role = c("aut", "cre"))
Description: A simple tool allowing users to easily and dynamically explore or document a data set using a tree structure.
URL: https://github.com/alforj/muir
BugReports: https://github.com/alforj/muir/issues
Depends: R (>= 3.1.2)
License: GPL (>= 2)
LazyData: true
Imports: DiagrammeR (>= 0.6), dplyr (>= 0.4.1), stringr (>= 0.6.2)
Suggests: htmlwidgets (>= 0.3.2)
Packaged: 2015-05-02 14:32:36 UTC; alforj
Author: Justin Alford [aut, cre]
Maintainer: Justin Alford
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-02 16:46:05

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New package pogit with initial version 1.0.0
Package: pogit
Type: Package
Title: Bayesian Variable Selection for a Poisson-Logistic Model
Version: 1.0.0
Date: 2015-05-01
Authors@R: c(person("Michaela", "Dvorzak", role = c("aut","cre"), email = "m.dvorzak@gmx.at"), person("Helga", "Wagner", role = "aut"))
Author: Michaela Dvorzak [aut, cre], Helga Wagner [aut]
Maintainer: Michaela Dvorzak
Description: Bayesian variable selection for regression models of under-reported count data as well as for Poisson and binomial logit regression models using spike and slab priors.
License: GPL-2
Depends: R(>= 2.10.0)
Imports: BayesLogit, ggplot2, logistf, plyr
LazyData: true
NeedsCompilation: no
Packaged: 2015-05-02 12:21:14 UTC; michi
Repository: CRAN
Date/Publication: 2015-05-02 15:01:52

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New package mixtNB with initial version 1.0
Package: mixtNB
Type: Package
Title: DE Analysis of RNA-Seq Data by Mixtures of NB
Version: 1.0
Date: 2015-05-01
Author: Elisabetta Bonafede, Cinzia Viroli
Maintainer: Cinzia Viroli
Description: Differential expression analysis of RNA-Seq data when replicates under two conditions are available is performed. First, mixtures of Negative Binomial distributions are fitted on the data in order to estimate the dispersions, then the Wald test is computed.
License: GPL-3
Packaged: 2015-05-02 08:27:32 UTC; viroli
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-02 14:11:25

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