Mon, 02 Feb 2015

New package spatialEco with initial version 0.1-0
Package: spatialEco
Type: Package
Title: Spatial Analysis and Modeling
Version: 0.1-0
Date: 2015-02-02
Authors@R: c(person(family="Evans", given="Jeffrey S.", email = "jeffrey_evans@tnc.org", role = c("aut", "cre")), person(family="Ram", given="Karthik", role = "ctb") )
Description: Utilities to support spatial data manipulation, query, sampling and modeling. Functions include models for species population density, download utilities for climate and global deforestation spatial products, spatial smoothing, multivariate separability, point process model for creating pseudo-absences and subsampling, polygon and point-distance landscape metrics, auto-logistic model, sampling models, cluster optimization and statistical exploratory tools.
Depends: R (>= 3.1.0)
Imports: RANN, rms, sp (>= 1.0-15), raster (>= 2.3-10), spatstat (>= 1.35-0), cluster, spdep, SDMTools, RCurl, rgeos
Maintainer: Jeffrey S. Evans
License: GPL-3
URL: http://evansmurphy.wix.com/evansspatial
NeedsCompilation: no
Repository: CRAN
LazyData: true
Packaged: 2015-02-02 21:43:22 UTC; jevans
Author: Jeffrey S. Evans [aut, cre], Karthik Ram [ctb]
Date/Publication: 2015-02-02 23:10:33

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New package SETPath with initial version 1.0
Package: SETPath
Type: Package
Title: Spiked Eigenvalue Test for Pathway data
Version: 1.0
Date: 2014-12-26
Author: Patrick Danaher
Maintainer: Patrick Danaher
Description: Tests gene expression data from a biological pathway for biologically meaningful differences in the eigenstructure between two classes. Specifically, it tests the null hypothesis that the two classes' leading eigenvalues and sums of eigenvalues are equal. A pathway's leading eigenvalue arguably represents the total variability due to variability in pathway activity, while the sum of all its eigenvalues represents the variability due to pathway activity and to other, unregulated causes. Implementation of the method described in Danaher (2015), "Covariance-based analyses of biological pathways".
License: GPL-2
Packaged: 2015-02-02 20:03:46 UTC; pdanaher
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-02 22:37:42

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New package poisDoubleSamp with initial version 1.0
Package: poisDoubleSamp
Version: 1.0
Date: 2015-02-02
Title: Confidence Intervals with Poisson Double Sampling
Description: Functions to create confidence intervals for ratios of Poisson rates under misclassification using double sampling.
URL: https://github.com/dkahle/poisDoubleSamp
BugReports: https://github.com/dkahle/poisDoubleSamp/issues
Authors@R: c(person("David", "Kahle", email = "david.kahle@gmail.com", role = c("aut", "cre")), person("Phil", "Young", email = "philip_young@baylor.edu", role = "aut"), person("Dean", "Young", email = "dean_young@baylor.edu", role = "aut"))
LinkingTo: Rcpp
Imports: Rcpp
License: GPL-2
LazyData: true
Packaged: 2015-02-02 19:47:51 UTC; david_kahle
Author: David Kahle [aut, cre], Phil Young [aut], Dean Young [aut]
Maintainer: David Kahle
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-02 22:41:55

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Package lmeNB updated to version 1.3 with previous version 1.2 dated 2014-01-24

Title: Compute the Personalized Activity Index Based on a Negative Binomial Model
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "Detection of unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Zhao, Y., Li, D.K.B., Petkau, A.J., Riddehough, A., Traboulsee, A., published in Journal of the American Statistical Association in 2013. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which can be modelled with a gamma or log-normal distributions. One can also choose the semi-parametric option which does not assume any distribution for the random effect. These mixed-effect models could be useful beyond the application of the safety monitoring. The maximum likelihood methods are used to estimate the unknown fixed effect parameters of the model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNBBayes, which contains the functions to compute the Personalized Activity Index in Bayesian framework.
Author: Yinshan Zhao and Yumi Kondo (with contributions from Steven G. Johnson, Rudolf Schuerer and Brian Gough on the integration subroutines)
Maintainer: Yumi Kondo

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New package LeafArea with initial version 0.0.5
Package: LeafArea
Type: Package
Title: A Rapid Digital Image Analysis for Leaf Area
Version: 0.0.5
Date: 2015-02-02
Author: Masatoshi Katabuchi
Maintainer: Masatoshi Katabuchi
Description: An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes. This package includes function to write an ImageJ macro which is optimized for a leaf area analysis by default.
SystemRequirements: ImageJ 1.48 (see http://imagej.nih.gov/ij/)
License: GPL-2
Packaged: 2015-02-02 19:48:02 UTC; mattocci
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-02 22:33:50

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Package excursions updated to version 2.0.6 with previous version 1.1-20140610 dated 2014-06-11

Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin and Finn Lindgren
Maintainer: David Bolin

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Package CRTSize updated to version 0.4 with previous version 0.3 dated 2013-12-18

Title: Sample Size Estimation Functions for Cluster Randomized Trials
Description: This package contains basic tools for the purpose of sample size estimation in cluster (group) randomized trials. The package contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
Author: Michael A Rotondi
Maintainer: Michael A Rotondi

Diff between CRTSize versions 0.3 dated 2013-12-18 and 0.4 dated 2015-02-02

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Package simMSM updated to version 1.1.4 with previous version 1.1.2 dated 2015-01-12

Title: Simulation of Event Histories for Multi-state Models
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions, and dependencies on the past of the history. Random generation of event histories is performed using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen

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New package Rsampletrees with initial version 0.1
Package: Rsampletrees
Type: Package
Title: Sampletrees Input/Output Processing
Description: Contains functions that are useful for pre- and post-processing the tree output from the MCMC-based C++ program sampletrees. The program sampletrees is used to sample gene genealogies conditional on either phased or unphased SNP genotype data. More information about sampletrees can be found at http://stat.sfu.ca/statgen/research/sampletrees.html . Pre-processing tasks involve creating the settings file, the haplotype estimation files (if input data is genotype), and error checking the settings. Post-processing involves reading in the MCMC output from a run of sampletrees and computing summary statistics.
Version: 0.1
Date: 2014-08-01
Author: Kelly Burkett, Brad McNeney, Jinko Graham
Maintainer: Kelly Burkett
Depends: haplo.stats, ape
License: GPL-2
Packaged: 2015-02-02 18:50:40 UTC; kellyburkett
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-02 20:45:11

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Package relations updated to version 0.6-4 with previous version 0.6-3 dated 2014-04-02

Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Author: David Meyer [aut], Kurt Hornik [aut, cre], Christian Buchta [ctb]
Maintainer: Kurt Hornik

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Package clue updated to version 0.3-49 with previous version 0.3-48 dated 2014-04-02

Title: Cluster ensembles
Description: CLUster Ensembles
Author: Kurt Hornik [aut, cre], Walter Böhm [ctb]
Maintainer: Kurt Hornik

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Package twang updated to version 1.4-9.3 with previous version 1.4-0 dated 2014-03-18

Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: This package offers functions for propensity score estimating and weighting, nonresponse weighting, and diagnosis of the weights. This package was originally developed by Drs. Ridgeway, McCaffrey, and Morral. Burgette, Griffin and McCaffrey updated the package during 2011-2015.
Author: Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann, Lane Burgette
Maintainer: Lane Burgette

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Package sjPlot updated to version 1.6.8 with previous version 1.6.5 dated 2014-12-15

Title: Data Visualization for Statistics in Social Science
Description: Collection of several plotting and table output functions for visualizing data, and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke

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Package BrailleR updated to version 0.16.1 with previous version 0.11 dated 2014-09-27

Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], Paul Murrell [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey

Diff between BrailleR versions 0.11 dated 2014-09-27 and 0.16.1 dated 2015-02-02

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Package visova (with last version 1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-08-22 1.1
2014-08-09 1.0

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Package textreg updated to version 0.1.1 with previous version 0.1 dated 2014-12-04

Title: n-gram Text Regression, aka Concise Comparative Summarization
Description: Function for sparse regression on raw text, regressing a labeling vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix

Diff between textreg versions 0.1 dated 2014-12-04 and 0.1.1 dated 2015-02-02

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Package strum updated to version 0.5.1 with previous version 0.5 dated 2014-12-10

Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: This package implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre], Yeunjoo Song [aut], Stephen Cahn [ctb]
Maintainer: Nathan Morris

Diff between strum versions 0.5 dated 2014-12-10 and 0.5.1 dated 2015-02-02

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Package royston updated to version 1.2 with previous version 1.1 dated 2015-01-16

Title: Royston's H Test: Multivariate Normality Test
Description: Performs a multivariate normality test based on Royston's H test
Author: Selcuk Korkmaz
Maintainer: Selcuk Korkmaz

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Package RGA updated to version 0.2 with previous version 0.1.4 dated 2014-12-19

Title: A Google Analytics API client for R
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also package provides shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov

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Package tripEstimation updated to version 0.0-42 with previous version 0.0-41 dated 2013-07-10

Title: Metropolis Sampler and Supporting Functions for Estimating Animal Movement from Archival Tags and Satellite Fixes
Description: Data handling and estimation functions for animal movement estimation from archival or satellite tags. Helper functions are included for making image summaries binned by time interval from MCMC simulations of point data.
Author: Michael D. Sumner [aut, cre], Simon Wotherspoon [ctb]
Maintainer: Michael D. Sumner

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Package ASMap updated to version 0.3-3 with previous version 0.3-2 dated 2014-10-13

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor , David Butler .
Maintainer: Julian Taylor

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Package abd updated to version 0.2-7 with previous version 0.2-6 dated 2014-03-31

Title: The Analysis of Biological Data
Description: The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Author: Kevin M. Middleton , Randall Pruim
Maintainer: Kevin M. Middleton

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 man/PrimateWBC.Rd            |   11 -
 man/ProgesteroneExercise.Rd  |   18 +-
 man/Pseudoscorpions.Rd       |   20 +-
 man/Pufferfish.Rd            |   22 +--
 man/Rattlesnakes.Rd          |   16 +-
 man/Rigormortis.Rd           |   13 -
 man/RopeTrick.Rd             |   16 +-
 man/SagebrushCrickets.Rd     |   17 +-
 man/SalmonColor.Rd           |   20 +-
 man/Seedlings.Rd             |    6 
 man/Selection.Rd             |   18 +-
 man/SexualSelection.Rd       |   21 +-
 man/ShadParasites.Rd         |   14 -
 man/ShrinkingSeals.Rd        |   16 +-
 man/ShuttleDisaster.Rd       |   22 +--
 man/Silversword.Rd           |   14 -
 man/SleepAndPerformance.Rd   |   15 +-
 man/SockeyeFemales.Rd        |   17 +-
 man/Sparrows.Rd              |   17 +-
 man/SpiderColonies.Rd        |   15 --
 man/SpiderSpeed.Rd           |   20 +-
 man/Stalkies1.Rd             |    9 -
 man/Stalkies2.Rd             |   16 +-
 man/SticklebackPlates.Rd     |   32 ++--
 man/SticklebackPreference.Rd |   19 +-
 man/Sumo.Rd                  |   11 -
 man/SyrupSwimming.Rd         |   17 +-
 man/TeenDeaths.Rd            |   15 --
 man/Telomeres.Rd             |   18 +-
 man/TimeOfDeath.Rd           |   14 -
 man/Toads.Rd                 |    9 -
 man/Tobacco.Rd               |   16 +-
 man/Tobacco2.Rd              |   18 +-
 man/ToothAge.Rd              |   15 +-
 man/TreeSeedlings.Rd         |   16 +-
 man/Trematodes.Rd            |   15 +-
 man/Trillium.Rd              |   15 +-
 man/Truffles.Rd              |   20 +-
 man/TsetseLearning.Rd        |   16 +-
 man/TwoKids.Rd               |   13 -
 man/VampireBites.Rd          |    9 -
 man/VasopressinVoles.Rd      |   20 +-
 man/Vines.Rd                 |   16 +-
 man/VoleDispersal.Rd         |   12 -
 man/WalkingStickFemurs.Rd    |   17 +-
 man/WalkingStickHeads.Rd     |   20 +-
 man/WeddellSeals.Rd          |   19 +-
 man/WillsDebates.Rd          |    9 -
 man/WillsPresidents.Rd       |   11 -
 man/WolfTeeth.Rd             |   18 +-
 man/Wolves.Rd                |   17 +-
 man/WorldCup.Rd              |    5 
 man/WrasseSexes.Rd           |    6 
 man/YeastGenes.Rd            |   12 -
 man/ZebraFinchBeaks.Rd       |   17 +-
 man/ZebraFinches.Rd          |   17 +-
 man/ZooMortality.Rd          |   13 -
 man/Zooplankton.Rd           |   19 +-
 man/abd-package.Rd           |   30 ++--
 man/abdData.Rd               |   45 ++----
 man/dataInfo.Rd              |    9 -
 man/histochart.Rd            |   32 +---
 man/themes.Rd                |   28 +--
 156 files changed, 1455 insertions(+), 1693 deletions(-)

More information about abd at CRAN
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