Tue, 27 Sep 2016

Package sbtools updated to version 1.1.6 with previous version 1.1.3 dated 2016-08-19

Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
Author: Tim Kern [cre], Luke Winslow [aut], Scott Chamberlain [aut], Alison Appling [aut], Jordan Read [aut]
Maintainer: Tim Kern <kernt@usgs.gov>

Diff between sbtools versions 1.1.3 dated 2016-08-19 and 1.1.6 dated 2016-09-27

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New package scdhlm with initial version 0.3
Package: scdhlm
Title: Estimating Hierarchical Linear Models for Single-Case Designs
Version: 0.3
Authors@R: person("James", "Pustejovsky", email = "jepusto@gmail.com", role = c("aut", "cre"))
Description: Provides a set of tools for estimating hierarchical linear models and effect sizes based on data from single-case designs. Functions are provided for calculating standardized mean difference effect sizes that are directly comparable to standardized mean differences estimated from between-subjects randomized experiments, as described in Hedges, Pustejovsky, and Shadish (2012) <DOI:10.1002/jrsm.1052>; Hedges, Pustejovsky, and Shadish (2013) <DOI:10.1002/jrsm.1086>; and Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>.
URL: https://github.com/jepusto/scdhlm
BugReports: https://github.com/jepusto/scdhlm/issues
License: GPL-3
VignetteBuilder: knitr
LazyData: true
Imports: stats
Depends: nlme, R (>= 3.0.1)
Suggests: knitr, markdown, rmarkdown, ggplot2, plyr, boot, parallel, shiny, testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-09-27 15:33:19 UTC; jep2963
Author: James Pustejovsky [aut, cre]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Repository: CRAN
Date/Publication: 2016-09-27 21:29:27

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New package RNHANES with initial version 1.0
Package: RNHANES
Type: Package
Title: Facilitates Analysis of CDC NHANES Data
Version: 1.0
Date: 2016-09-27
Authors@R: c( person("Herb", "Susmann", email="susmann@silentspring.org", role=c("cre", "aut")), person("Silent Spring Institute", role = "cph") )
URL: http://github.com/silentspringinstitute/RNHANES
BugReports: https://github.com/silentspringinstitute/RNHANES/issues
Description: Tools for downloading and analyzing CDC NHANES data, with a focus on analytical laboratory data.
License: Apache License 2.0 | file LICENSE
LazyData: TRUE
Depends: R (>= 2.10)
Imports: foreign, survey, rvest, xml2, methods, dplyr
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-09-27 15:21:07 UTC; susmann
Author: Herb Susmann [cre, aut], Silent Spring Institute [cph]
Maintainer: Herb Susmann <susmann@silentspring.org>
Repository: CRAN
Date/Publication: 2016-09-27 21:32:39

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Package PCGSE updated to version 0.3 with previous version 0.2 dated 2014-05-07

Title: Principal Component Gene Set Enrichment
Description: Contains logic for computing the statistical association of variable groups, i.e., gene sets, with respect to the principal components of genomic data.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>

Diff between PCGSE versions 0.2 dated 2014-05-07 and 0.3 dated 2016-09-27

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Package DynNom updated to version 3.0.1 with previous version 3.0 dated 2016-09-20

Title: Dynamic Nomograms for Linear, Generalized Linear and Proportional Hazard Models
Description: Demonstrate the results of a statistical model object as a dynamic nomogram in an 'RStudio' panel or web browser. DynNom supports a variety of model objects; 'lm', 'glm', 'coxph' and also 'Ols', 'Glm', 'lrm', 'cph' models.
Author: Amirhossein Jalali, Davood Roshan, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>

Diff between DynNom versions 3.0 dated 2016-09-20 and 3.0.1 dated 2016-09-27

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Package blavaan updated to version 0.2-2 with previous version 0.2-1 dated 2016-09-20

Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre], Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>

Diff between blavaan versions 0.2-1 dated 2016-09-20 and 0.2-2 dated 2016-09-27

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Package berryFunctions updated to version 1.12.3 with previous version 1.12.2 dated 2016-09-21

Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>

Diff between berryFunctions versions 1.12.2 dated 2016-09-21 and 1.12.3 dated 2016-09-27

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Package GameTheory updated to version 2.4 with previous version 2.0 dated 2015-08-10

Title: Cooperative Game Theory
Description: Implementation of a common set of punctual solutions for Cooperative Game Theory.
Author: Sebastian Cano-Berlanga
Maintainer: Sebastian Cano-Berlanga <cano.berlanga@gmail.com>

Diff between GameTheory versions 2.0 dated 2015-08-10 and 2.4 dated 2016-09-27

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Package sjPlot updated to version 2.1.0 with previous version 2.0.2 dated 2016-07-31

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjPlot versions 2.0.2 dated 2016-07-31 and 2.1.0 dated 2016-09-27

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Package SIDES updated to version 1.6 with previous version 1.5 dated 2016-09-15

Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between SIDES versions 1.5 dated 2016-09-15 and 1.6 dated 2016-09-27

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Package qwraps2 updated to version 0.2.2 with previous version 0.2.1 dated 2016-05-30

Title: Quick Wraps 2
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 a 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'.
Author: Peter DeWitt [aut, cre], Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>

Diff between qwraps2 versions 0.2.1 dated 2016-05-30 and 0.2.2 dated 2016-09-27

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Package nontarget updated to version 1.9 with previous version 1.8 dated 2016-03-14

Title: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos <mloos@looscomputing.ch>

Diff between nontarget versions 1.8 dated 2016-03-14 and 1.9 dated 2016-09-27

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Package funrar updated to version 1.0.1 with previous version 1.0.0 dated 2016-07-15

Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al (accepted). Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity.
Author: Matthias Grenié [aut, cre], Pierre Denelle [aut], Caroline Tucker [aut]
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>

Diff between funrar versions 1.0.0 dated 2016-07-15 and 1.0.1 dated 2016-09-27

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New package exprso with initial version 0.1.7
Package: exprso
Title: Rapid Implementation of Machine Learning Algorithms for Genomic Data
Version: 0.1.7
URL: http://github.com/tpq/exprso
BugReports: http://github.com/tpq/exprso/issues
Authors@R: c( person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")), person("Daniel", "Tylee", email = "dantylee@gmail.com", role = "ctb") )
Description: Supervised machine learning has an increasingly important role in biological studies. However, the sheer complexity of classification pipelines poses a significant barrier to the expert biologist unfamiliar with machine learning. Moreover, many biologists lack the time or technical skills necessary to establish their own pipelines. This package introduces a framework for the rapid implementation of high-throughput supervised machine learning built with the biologist user in mind. Written by biologists, for biologists, this package provides a user-friendly interface that empowers investigators to execute state-of-the-art binary and multi-class classification, including deep learning, with minimal programming experience necessary.
License: GPL-2
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Imports: cluster, MASS, e1071, lattice, methods, mRMRe, nnet, pathClass, plyr, stats, randomForest, ROCR, sampling
Depends: R (>= 3.2.2), kernlab
Suggests: Biobase, GEOquery, h2o, golubEsets, knitr, limma, magrittr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2016-09-27 07:00:17 UTC; thom
Author: Thomas Quinn [aut, cre], Daniel Tylee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Repository: CRAN
Date/Publication: 2016-09-27 16:39:46

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Package nproc updated to version 2.0.1 with previous version 1.2 dated 2016-08-11

Title: Neyman-Pearson Receiver Operating Characteristics
Description: Given a sample of class 0 and class 1 and a classification method, the package generates the corresponding Neyman-Pearson classifier with a pre-specified type-I error control and Neyman-Pearson Receiver Operating Characteristics.
Author: Yang Feng, Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>

Diff between nproc versions 1.2 dated 2016-08-11 and 2.0.1 dated 2016-09-27

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Package NHMM updated to version 3.6 with previous version 3.5 dated 2014-11-26

Title: Bayesian Non-Homogenous Markov and Mixture Models (Multiple Time Series)
Description: Bayesian HMM and NHMM modeling for multiple time series. The emission distribution can be mixtures of Gammas, Poissons, Normals and zero inflation is possible.
Author: Tracy Holsclaw
Maintainer: Tracy Holsclaw <iamrandom@iamrandom.com>

Diff between NHMM versions 3.5 dated 2014-11-26 and 3.6 dated 2016-09-27

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New package neurobase with initial version 1.1.1.1
Package: neurobase
Type: Package
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects
Version: 1.1.1.1
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Description: Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.
Imports: methods, matrixStats, R.utils, graphics, grDevices, stats, utils
Depends: oro.nifti (>= 0.5.0), R (>= 3.2.0)
License: GPL-2
Suggests: testthat
BugReports: https://github.com/muschellij2/nifti/issues
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2016-09-26 22:54:15 UTC; johnmuschelli
Repository: CRAN
Date/Publication: 2016-09-27 08:41:48

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Package ecp updated to version 3.0.0 with previous version 2.0.0 dated 2015-05-20

Title: Non-Parametric Multiple Change-Point Analysis of Multivariate Data
Description: Implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and probabilistic pruning, with no distributional assumptions other than the existence of certain absolute moments in one method. Hierarchical and exact search methods are included. All methods return the set of estimated change- points as well as other summary information.
Author: Nicholas A. James, Wenyu Zhang and David S. Matteson
Maintainer: Nicholas A. James <nj89@cornell.edu>

Diff between ecp versions 2.0.0 dated 2015-05-20 and 3.0.0 dated 2016-09-27

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Package corHMM updated to version 1.20 with previous version 1.19 dated 2016-06-13

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 <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>

Diff between corHMM versions 1.19 dated 2016-06-13 and 1.20 dated 2016-09-27

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