Wed, 08 Apr 2015

New package phenology with initial version 4.1
Package: phenology
Type: Package
Title: Tools to Manage a Parametric Function that Describes Phenology
Version: 4.1
Date: 2015-04-08
Author: Marc Girondot
Maintainer: Marc Girondot
Depends: fields, zoo, coda, HelpersMG, shiny, R (>= 2.14.0)
Description: Functions used to fit and test the phenology of species based on counts.
License: GPL-2
LazyData: yes
LazyLoad: yes
URL: http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Marine_Turtles_Nesting_Season.html
Encoding: UTF-8
Packaged: 2015-04-08 15:03:36 UTC; marc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-09 01:18:00

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New package readr with initial version 0.1.0
Package: readr
Version: 0.1.0
Title: Read Tabular Data
Description: Read flat/tabular text files from disk.
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", c("aut", "cre")), person("Romain", "Francois", role = "aut"), person("R Core Team", role = "ctb", comment = "Date time code adapted from R"), person("RStudio", role = "cph"))
Encoding: UTF-8
Depends: R (>= 3.0.2)
LinkingTo: Rcpp, BH
Imports: Rcpp (>= 0.11.5), curl
Suggests: testthat, knitr, DiagrammeR
License: GPL (>= 2)
VignetteBuilder: knitr
Packaged: 2015-04-08 20:31:26 UTC; hadley
Author: Hadley Wickham [aut, cre], Romain Francois [aut], R Core Team [ctb] (Date time code adapted from R), RStudio [cph]
Maintainer: Hadley Wickham
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-09 01:03:53

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New package qwraps2 with initial version 0.1
Package: qwraps2
Title: Quick Wraps 2
Version: 0.1
Authors@R: person("Peter", "DeWitt", , "dewittpe@gmail.com", role = c("aut", "cre"))
Description: A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into .Rnw or .Rmd files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of an package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at https://github.com/dewittpe/qwraps. The implementation and limited scope of the functions within 'qwraps2' (https://github.com/dewittpe/qwraps2) is fundamentally different from 'qwraps'.
Depends: R (>= 3.1.3)
License: GPL-2
LazyData: true
Imports: dplyr, ggplot2
Packaged: 2015-04-08 16:48:55 UTC; dewittp
Author: Peter DeWitt [aut, cre]
Maintainer: Peter DeWitt
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-09 00:40:15

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Package isa2 updated to version 0.3.4 with previous version 0.3.3 dated 2013-09-24

Title: The Iterative Signature Algorithm
Description: The ISA is a biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Author: Gabor Csardi
Maintainer: Gabor Csardi

Diff between isa2 versions 0.3.3 dated 2013-09-24 and 0.3.4 dated 2015-04-08

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Package haven updated to version 0.2.0 with previous version 0.1.1 dated 2015-03-03

Title: Import SPSS, Stata and SAS Files
Description: Import foreign statistical formats into R via the embedded ReadStat C library (https://github.com/WizardMac/ReadStat). Package includes preliminary support for writing Stata and SPSS formats.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), RStudio [cph]
Maintainer: Hadley Wickham

Diff between haven versions 0.1.1 dated 2015-03-03 and 0.2.0 dated 2015-04-08

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Package falsy updated to version 1.0.1 with previous version 1.0 dated 2014-08-27

Title: Define Truthy and Falsy Values
Description: A value is falsy if it is NULL, FALSE, the empty string, zero, or an empty vector or list. Other values are truthy. The new %&&% and %||% operators work with falsy and truthy values and can be used for concise conditional execution.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi

Diff between falsy versions 1.0 dated 2014-08-27 and 1.0.1 dated 2015-04-08

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New package groupRemMap with initial version 0.1-0
Package: groupRemMap
Version: 0.1-0
Date: 2015-03-25
Title: Regularized Multivariate Regression for Identifying Master Predictors Using the GroupRemMap Penalty
Author: Xianlong Wang , Li Qin, Hexin Zhang, Yuzheng Zhang, Li Hsu, Pei Wang
Maintainer: Xianlong Wang
Description: An implementation of the GroupRemMap penalty for fitting regularized multivariate response regression models under the high-dimension-low-sample-size setting. When the predictors naturally fall into groups, the GroupRemMap penalty encourages procedure to select groups of predictors, while control for the overall sparsity of the final model.
License: GPL (>= 2)
Packaged: 2015-04-08 16:58:29 UTC; xwan2
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-09 01:07:16

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Package crayon updated to version 1.2.0 with previous version 1.1.0 dated 2014-10-15

Title: Colored Terminal Output
Description: Colored terminal output on terminals that support ANSI color and highlight codes. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the chalk JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi

Diff between crayon versions 1.1.0 dated 2014-10-15 and 1.2.0 dated 2015-04-08

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Package hsdar updated to version 0.1.2 with previous version 0.1.1 dated 2015-03-25

Title: Manage, Analyse and Simulate Hyperspectral Data in R
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using PROSPECT and PROSAIL.
Author: Lukas W. Lehnert [cre, aut], Hanna Meyer [ctb], Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert

Diff between hsdar versions 0.1.1 dated 2015-03-25 and 0.1.2 dated 2015-04-08

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Package heatmap3 updated to version 1.1.1 with previous version 1.0.7 dated 2014-08-29

Title: An Improved Heatmap Package
Description: An improved heatmap package. Completely compatible with the original R function heatmap, and provides more powerful and convenient features.
Author: Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao

Diff between heatmap3 versions 1.0.7 dated 2014-08-29 and 1.1.1 dated 2015-04-08

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Package DVHmetrics updated to version 0.2 with previous version 0.1 dated 2015-01-29

Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics, gEUD, NTCP, TCP, show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre], Heiko Karle [aut], Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger

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Package wux updated to version 2.0-0 with previous version 1.2-3 dated 2015-02-06

Title: Wegener Center Climate Uncertainty Explorer
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik

Diff between wux versions 1.2-3 dated 2015-02-06 and 2.0-0 dated 2015-04-08

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Package RxnSim updated to version 1.0.1 with previous version 1.0 dated 2015-03-12

Title: Functions to Compute Chemical Reaction Similarity
Description: Methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages 'rCDK' and 'fingerprint' for cheminformatics functionality.
Author: Varun Giri [aut, cre]
Maintainer: Varun Giri

Diff between RxnSim versions 1.0 dated 2015-03-12 and 1.0.1 dated 2015-04-08

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Permanent link

New package retrosheet with initial version 1.0
Package: retrosheet
Type: Package
Title: Import 'Retrosheet' Data as a Structured R Object
Version: 1.0
Authors@R: c(person("Richard", "Scriven", email = "rmscriven@gmail.com", role = c("aut", "cre")), person("Ananda", "Mahto", email = "mrdwab@gmail.com", role = "ctb"))
Date: 2015-03-17
Maintainer: Richard Scriven
Description: A collection of tools for importing the professional baseball data available from http://www.retrosheet.org. In particular, the event (play-by-play) files can be especially difficult to parse. This package does the parsing on those files, returning the requested event as a structured R object. It will also retrieve the game-log, roster, and schedule files if requested.
URL: http://github.com/rmscriven/retrosheet
Depends: R (>= 2.10)
License: GPL (>= 2)
Imports: RCurl (>= 1.95-4.5), XML (>= 3.98-1.1), data.table(>= 1.9.4)
Note: Notice regarding the transfer of data from Retrosheet: The information used here was obtained free of charge from and is copyrighted by Retrosheet. Interested parties may contact Retrosheet at "www.retrosheet.org".
Packaged: 2015-04-08 05:54:37 UTC; richard
Author: Richard Scriven [aut, cre], Ananda Mahto [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 12:17:55

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Package RDML updated to version 0.8-3 with previous version 0.8-2 dated 2015-04-07

Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages.
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh

Diff between RDML versions 0.8-2 dated 2015-04-07 and 0.8-3 dated 2015-04-08

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Package pendensity updated to version 0.2.8 with previous version 0.2.7 dated 2014-02-25

Title: Density Estimation with a Penalized Mixture Approach
Description: Estimation of univariate (conditional) densities using penalized B-splines with automatic selection of optimal smoothing parameter.
Author: Christian Schellhase
Maintainer: Christian Schellhase

Diff between pendensity versions 0.2.7 dated 2014-02-25 and 0.2.8 dated 2015-04-08

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New package pairsD3 with initial version 0.0.6
Package: pairsD3
Title: D3 Scatterplot Matrices
Version: 0.0.6
Authors@R: person("Garth", "Tarr", , "garth.tarr@gmail.com", role = c("aut", "cre"))
Description: Creates an interactive scatterplot matrix using the D3 JavaScript library. See for more information on D3.
Depends: R (>= 3.1.2)
License: GPL (>= 3)
Date: 2015-04-08
URL: http://github.com/garthtarr/pairsD3/
LazyData: true
Imports: htmlwidgets (>= 0.3.2), shiny
Suggests: knitr
Packaged: 2015-04-08 09:31:43 UTC; garthtarr
Author: Garth Tarr [aut, cre]
Maintainer: Garth Tarr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 11:53:10

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Package partykit updated to version 1.0-1 with previous version 1.0-0 dated 2015-02-21

Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources (rpart, RWeka, PMML) yielding objects that share functionality for print/plot/predict methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree) and model-based recursive partitioning (mob) from the party package are provided based on the new infrastructure.
Author: Torsten Hothorn [aut, cre], Achim Zeileis [aut]
Maintainer: Torsten Hothorn

Diff between partykit versions 1.0-0 dated 2015-02-21 and 1.0-1 dated 2015-04-08

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Package glmnet updated to version 2.0-1 with previous version 1.9-8 dated 2014-05-24

Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie

Diff between glmnet versions 1.9-8 dated 2014-05-24 and 2.0-1 dated 2015-04-08

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New package TROM with initial version 1.0
Package: TROM
Type: Package
Title: Transcriptome Overlap Measure
Version: 1.0
Date: 2015-04-07
Author: Jingyi Jessica Li , Wei Li
Maintainer: Jingyi Jessica Li
Depends: R (>= 2.10), lattice, methods, topGO
Imports: AnnotationDbi, openxlsx, GO.db, gtools, RColorBrewer, gplots
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples.
License: GPL-2
Packaged: 2015-04-08 03:21:23 UTC; Think
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 07:25:04

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Package rSPACE updated to version 1.1.1 with previous version 1.1.0 dated 2015-02-28

Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis

Diff between rSPACE versions 1.1.0 dated 2015-02-28 and 1.1.1 dated 2015-04-08

 DESCRIPTION               |    6 +++---
 MD5                       |   10 +++++-----
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Permanent link

New package cqrReg with initial version 1.2
Package: cqrReg
Type: Package
Title: Quantile, Composite Quantile Regression and Regularized Versions
Version: 1.2
Date: 2015-04-07
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
License: GPL (>= 2)
Depends: Rcpp (>= 0.10.0),quantreg,R (>= 2.6)
LinkingTo: Rcpp,RcppArmadillo
NeedsCompilation: yes
Packaged: 2015-04-07 23:31:21 UTC; billy
Repository: CRAN
Date/Publication: 2015-04-08 07:35:09

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Package corHMM updated to version 1.16 with previous version 1.15 dated 2014-09-18

Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu , Jeffrey C. Oliver , Brian O'Meara
Maintainer: Jeremy Beaulieu

Diff between corHMM versions 1.15 dated 2014-09-18 and 1.16 dated 2015-04-08

 DESCRIPTION   |   14 +++---
 MD5           |   10 ++--
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More information about corHMM at CRAN
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Package ClickClust updated to version 1.1.4 with previous version 1.1.3 dated 2014-11-24

Title: Model-Based Clustering of Categorical Sequences
Description: Clustering categorical sequences by means of finite mixtures with Markov model components is the main utility of ClickClust. The package also allows detecting blocks of equivalent states by forward and backward state selection procedures.
Author: Volodymyr Melnykov [aut, cre]
Maintainer: Volodymyr Melnykov

Diff between ClickClust versions 1.1.3 dated 2014-11-24 and 1.1.4 dated 2015-04-08

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 ClickClust-1.1.4/ClickClust/demo/ConfidenceIntervals.R |only
 ClickClust-1.1.4/ClickClust/demo/DataSimulation.R      |only
 ClickClust-1.1.4/ClickClust/demo/EMalgorithm1.R        |only
 ClickClust-1.1.4/ClickClust/demo/EMalgorithm2.R        |only
 ClickClust-1.1.4/ClickClust/demo/ForwardSelection.R    |only
 ClickClust-1.1.4/ClickClust/demo/ReadData.R            |only
 ClickClust-1.1.4/ClickClust/demo/StatePrediction.R     |only
 ClickClust-1.1.4/ClickClust/demo/demoClickClust.R      |    2 
 ClickClust-1.1.4/ClickClust/demo/msnbc323.R            |only
 ClickClust-1.1.4/ClickClust/demo/utility.R             |    7 
 ClickClust-1.1.4/ClickClust/man/B3.Rd                  |only
 ClickClust-1.1.4/ClickClust/man/BackwardSearch.Rd      |    5 
 ClickClust-1.1.4/ClickClust/man/C.Rd                   |only
 ClickClust-1.1.4/ClickClust/man/ClickClust-package.Rd  |    2 
 ClickClust-1.1.4/ClickClust/man/ClickClust.Rd          |    2 
 ClickClust-1.1.4/ClickClust/man/ClickPlot.Rd           |   22 +
 ClickClust-1.1.4/ClickClust/man/ForwardSearch.Rd       |    5 
 ClickClust-1.1.4/ClickClust/man/Predict.Rd             |    2 
 ClickClust-1.1.4/ClickClust/man/ReadData.Rd            |   11 
 ClickClust-1.1.4/ClickClust/man/VarEst.Rd              |    2 
 ClickClust-1.1.4/ClickClust/man/msnbc323.Rd            |only
 ClickClust-1.1.4/ClickClust/man/synth.Rd               |only
 41 files changed, 318 insertions(+), 175 deletions(-)

More information about ClickClust at CRAN
Permanent link

Package CIDnetworks updated to version 0.8.1 with previous version 0.8.0 dated 2015-03-11

Title: Generative Models for Complex Networks with Conditionally Independent Dyadic Structure
Description: Generative models for complex networks with conditionally independent dyadic structure. Now supports directed arcs!
Author: Samrachana Adhikari [aut], Beau Dabbs [cre, aut], Brian Junker [aut], Mauricio Sadinle [aut], Tracy Sweet [aut], A.C. Thomas [aut]
Maintainer: Beau Dabbs

Diff between CIDnetworks versions 0.8.0 dated 2015-03-11 and 0.8.1 dated 2015-04-08

 DESCRIPTION         |    8 +--
 MD5                 |   21 ++++----
 NAMESPACE           |    1 
 R/CID-external.R    |   45 ++++++++++++++++-
 R/CID-gibbs.R       |  133 +++++++++++++++++++++++++++++++++++++++++-----------
 R/COV-reference.R   |   85 +++++++++++++++++++++++++--------
 R/SBM-reference.R   |    2 
 R/plotting-pieces.R |    8 +--
 data/Advice.RData   |only
 man/CID-data.Rd     |   13 ++++-
 man/CID-gibbs.Rd    |    4 -
 man/CID-master.Rd   |    3 -
 12 files changed, 252 insertions(+), 71 deletions(-)

More information about CIDnetworks at CRAN
Permanent link


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