Mon, 19 Sep 2016

Package regsem updated to version 0.4.0 with previous version 0.2.0 dated 2016-08-11

Title: Performs Regularization on Structural Equation Models
Description: Uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional SEM.
Author: Ross Jacobucci[aut,cre], Kevin J. Grimm [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>

Diff between regsem versions 0.2.0 dated 2016-08-11 and 0.4.0 dated 2016-09-19

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Package permPATH updated to version 1.0 with previous version 0.9 dated 2016-07-18

Title: Permutation Based Gene Expression Pathway Analysis
Description: Can be used to carry out permutation based gene expression pathway analysis. This work was supported by a National Institute of Allergy and Infectious Disease/National Institutes of Health contract (No. HHSN272200900059C).
Author: Ivo D. Shterev [aut, cre], Kouros Owzar [aut], Gregory D. Sempowski [aut], Kenneth Wilder [ctb, cph] (wrote original version of ranker.h)
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>

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Package memuse updated to version 3.0-1 with previous version 3.0-0 dated 2016-09-12

Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have? Learn the scintillating answer to these and many more such questions with the 'memuse' package.
Author: Drew Schmidt [aut, cre], Christian Heckendorf [ctb] (FreeBSD improvements to meminfo), Wei-Chen Chen [ctb] (Windows build fixes), Dan Burgess [ctb] (donation of a Mac for development and testing)
Maintainer: Drew Schmidt <wrathematics@gmail.com>

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Package fishmethods updated to version 1.10-0 with previous version 1.9-0 dated 2015-10-09

Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from published literature and contributions from colleagues.
Author: Gary A. Nelson <gary.nelson@state.ma.us>
Maintainer: Gary A. Nelson <gary.nelson@state.ma.us>

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Package CompQuadForm updated to version 1.4.2 with previous version 1.4.1 dated 2013-06-16

Title: Distribution Function of Quadratic Forms in Normal Variables
Description: Computes the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.
Author: P. Lafaye de Micheaux
Maintainer: P. Lafaye de Micheaux <lafaye@dms.umontreal.ca>

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Package broman updated to version 0.64-3 with previous version 0.62-1 dated 2016-01-05

Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to graphics (mostly for base graphics), permutation tests, running mean/median, and general utilities.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>

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Package TANDEM updated to version 1.0.0 with previous version 0.9.3 dated 2016-07-13

Title: A Two-Stage Approach to Maximize Interpretability of Drug Response Models Based on Multiple Molecular Data Types
Description: A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
Author: Nanne Aben
Maintainer: Nanne Aben <nanne.aben@gmail.com>

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Package sunburstR updated to version 0.6.2 with previous version 0.6.0 dated 2016-08-25

Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib, https://gist.github.com/kerryrodden/7090426), Kent Russell [aut, cre] (R interface), Florian Breitwieser [ctb] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

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Package shinythemes updated to version 1.1 with previous version 1.0.1 dated 2015-03-02

Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes from http://bootswatch.com/, which are packaged for use with Shiny applications.
Author: Winston Chang [aut, cre], RStudio [cph], Thomas Park [ctb, cph] (Bootswatch themes), Lukasz Dziedzic [ctb, cph] (Lato font), Nathan Willis [ctb, cph] (News Cycle font), Google Corporation [ctb, cph] (Open Sans font), Matt McInerney [ctb, cph] (Raleway font), Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font), Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang <winston@rstudio.com>

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Package rotl updated to version 3.0.1 with previous version 3.0.0 dated 2016-04-26

Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Author: Francois Michonneau [aut, cre], Joseph Brown [aut], David Winter [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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Package RNifti updated to version 0.2.0 with previous version 0.1.0 dated 2016-09-01

Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation between compiled C and interpreted R code. Not to be confused with RNiftyReg, which provides tools for image registration.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>

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Package msBP updated to version 1.2 with previous version 1.1 dated 2016-04-20

Title: Multiscale Bernstein Polynomials for Densities
Description: Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2016).
Author: Antonio Canale
Maintainer: Antonio Canale <antonio.canale@unito.it>

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Package MDMR updated to version 0.4.3 with previous version 0.4.2 dated 2016-08-12

Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>

Diff between MDMR versions 0.4.2 dated 2016-08-12 and 0.4.3 dated 2016-09-19

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Package IDSpatialStats updated to version 0.2.2 with previous version 0.2.1 dated 2016-05-10

Title: Estimate Global Clustering in Infectious Disease
Description: Implements various novel and standard clustering statistics and other analyses useful for understanding the spread of infectious disease.
Author: Justin Lessler <justin@jhu.edu>, Henrik Salje <hsalje@jhsph.edu>
Maintainer: Justin Lessler <justin@jhu.edu>

Diff between IDSpatialStats versions 0.2.1 dated 2016-05-10 and 0.2.2 dated 2016-09-19

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Package ggswissmaps updated to version 0.0.9 with previous version 0.0.8 dated 2016-02-12

Title: Offers Various Swiss Maps as ggplot2 Objects
Description: Offers various swiss maps as ggplot2 objects and gives the possibility to add layers of data on the maps. Data are publicly available from the swiss federal statistical office.
Author: Sandro Petrillo Burri [aut, cre], Eric Stephani [aut], Lisa Bottinelli [ctb]
Maintainer: Sandro Petrillo Burri <gibo.gaf@gmail.com>

Diff between ggswissmaps versions 0.0.8 dated 2016-02-12 and 0.0.9 dated 2016-09-19

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Package fuzzyjoin updated to version 0.1.2 with previous version 0.1.1 dated 2016-06-28

Title: Join Tables Together on Inexact Matching
Description: Join tables together based not on whether columns match exactly, but whether they are similar by some comparison. Implementations include string distance and regular expression matching.
Author: David Robinson [aut, cre], Joran Elias [ctb]
Maintainer: David Robinson <drobinson@stackoverflow.com>

Diff between fuzzyjoin versions 0.1.1 dated 2016-06-28 and 0.1.2 dated 2016-09-19

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New package UCR.ColumnNames with initial version 0.1.0
Package: UCR.ColumnNames
Type: Package
Title: Fixes Column Names for Uniform Crime Report "Offenses Known and Clearance by Arrest" Datasets
Version: 0.1.0
Authors@R: person("Jacob", "Kaplan", email = "jacobkap@sas.upenn.edu", role = c ("aut", "cre"))
Depends: R (>= 2.10)
Description: Changes the column names of the inputted dataset to the correct names from the Uniform Crime Report codebook for the "Offenses Known and Clearance by Arrest" datasets from 1998-2014.
License: GPL
LazyData: TRUE
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2016-09-19 13:05:40 UTC; user
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jacobkap@sas.upenn.edu>
Repository: CRAN
Date/Publication: 2016-09-19 16:04:42

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Package Rsomoclu updated to version 1.6.2.1 with previous version 1.6.2 dated 2016-08-11

Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>

Diff between Rsomoclu versions 1.6.2 dated 2016-08-11 and 1.6.2.1 dated 2016-09-19

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Package asymmetry updated to version 1.1.1 with previous version 1.1 dated 2016-06-25

Title: Visualizing Asymmetric Data
Description: The slide-vector model is provided in this package together with functions for the analysis and graphical display of asymmetry. The slide vector model is a scaling model for asymmetric data. A distance model is fitted to the symmetric part of the data whereas the asymmetric part of the data is represented by projections of the coordinates onto the slide-vector. The slide-vector points in the direction of large asymmetries in the data. The distance is modified in such a way that the distance between two points that are parallel to the slide-vector is larger in the direction of this vector. The distance is smaller in the opposite direction. If the line connecting two points is perpendicular to the slide-vector the difference between the two projections is zero. In this case the distance between the two points is symmetric. The algorithm for fitting this model is derived from the majorization approach to multidimensional scaling.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>

Diff between asymmetry versions 1.1 dated 2016-06-25 and 1.1.1 dated 2016-09-19

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Package fastcluster updated to version 1.1.21 with previous version 1.1.20 dated 2016-03-31

Title: Fast Hierarchical Clustering Routines for R and Python
Description: This is a two-in-one package which provides interfaces to both R and Python. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the SciPy package 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the 'flashClust' package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner <daniel@danifold.net>

Diff between fastcluster versions 1.1.20 dated 2016-03-31 and 1.1.21 dated 2016-09-19

 fastcluster-1.1.20/fastcluster/src/fastcluster_python.cpp        |only
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Package roll updated to version 1.0.6 with previous version 1.0.5 dated 2016-08-29

Title: Rolling Statistics
Description: Parallel functions for computing rolling statistics of time-series data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>

Diff between roll versions 1.0.5 dated 2016-08-29 and 1.0.6 dated 2016-09-19

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 NEWS.md             |    6 
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New package rakeR with initial version 0.1.1
Package: rakeR
Title: Easy Spatial Microsimulation (Raking) in R
Version: 0.1.1
Authors@R: c( person("Phil Mike", "Jones", email = "philmikejones@gmail.com", role = c("aut", "cre")), person("Robin", "Lovelace", role = "aut", comment = "Many functions are based on code by Robin Lovelace and Morgane Dumont"), person("Morgane", "Dumont", role = "aut", comment = "Many functions are based on code by Robin Lovelace and Morgane Dumont"))
Description: Functions for performing spatial microsimulation ('raking') in R.
Depends: R (>= 3.3.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Imports: ipfp
Suggests: testthat, readr
URL: https://github.com/philmikejones/rakeR
BugReports: https://github.com/philmikejones/rakeR/issues
NeedsCompilation: no
Packaged: 2016-09-19 09:04:03 UTC; ggp13pmj
Author: Phil Mike Jones [aut, cre], Robin Lovelace [aut] (Many functions are based on code by Robin Lovelace and Morgane Dumont), Morgane Dumont [aut] (Many functions are based on code by Robin Lovelace and Morgane Dumont)
Maintainer: Phil Mike Jones <philmikejones@gmail.com>
Repository: CRAN
Date/Publication: 2016-09-19 11:19:57

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Package mdhglm updated to version 1.6 with previous version 1.4 dated 2016-06-28

Title: Multivariate Double Hierarchical Generalized Linear Models
Description: Allows various models for multivariate response variables where each response is assumed to follow double hierarchical generalized linear models. In double hierarchical generalized linear models, the mean, dispersion parameters for variance of random effects, and residual variance can be further modeled as random-effect models.
Author: Youngjo Lee, Marek Molas, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>

Diff between mdhglm versions 1.4 dated 2016-06-28 and 1.6 dated 2016-09-19

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 R/hglmfit_corr.R       |    1 
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Package dhglm updated to version 1.6 with previous version 1.5 dated 2015-09-18

Title: Double Hierarchical Generalized Linear Models
Description: Double hierarchical generalized linear models in which the mean, dispersion parameters for variance of random effects, and residual variance (overdispersion) can be further modeled as random-effect models.
Author: Youngjo Lee, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>

Diff between dhglm versions 1.5 dated 2015-09-18 and 1.6 dated 2016-09-19

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Package marelac updated to version 2.1.6 with previous version 2.1.5 dated 2015-09-04

Title: Tools for Aquatic Sciences
Description: Datasets, constants, conversion factors, and utilities for 'MArine', 'Riverine', 'Estuarine', 'LAcustrine' and 'Coastal' science. The package contains among others: (1) chemical and physical constants and datasets, e.g. atomic weights, gas constants, the earths bathymetry; (2) conversion factors (e.g. gram to mol to liter, barometric units, temperature, salinity); (3) physical functions, e.g. to estimate concentrations of conservative substances, gas transfer and diffusion coefficients, the Coriolis force and gravity; (4) thermophysical properties of the seawater, as from the UNESCO polynomial or from the more recent derivation based on a Gibbs function.
Author: Karline Soetaert <karline.soetaert@nioz.nl>, Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>, Filip Meysman <filip.meysman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

Diff between marelac versions 2.1.5 dated 2015-09-04 and 2.1.6 dated 2016-09-19

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Package FREGAT updated to version 1.0.2 with previous version 1.0.1 dated 2016-04-12

Title: Family REGional Association Tests
Description: Fast regional association analysis of quantitative traits for family-based and population studies.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and Gulnara R. Svishcheva <gulsvi@mail.ru>, with contributions from: Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method), Thomas Lumley ('kuonen' method), James O. Ramsay (functional data analysis functions), David Clayton ('read.plink' function) and Brian Ripley ('ginv' function)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>

Diff between FREGAT versions 1.0.1 dated 2016-04-12 and 1.0.2 dated 2016-09-19

 DESCRIPTION           |    6 ++---
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New package htdp with initial version 0.1.4
Package: htdp
Type: Package
Title: Horizontal Time Dependent Positioning
Version: 0.1.4
Date: 2016-09-19
Authors@R: c( person("John", "Buonagurio", , "jbuonagurio@exponent.com", role = c("aut", "cre")), person("National Geodetic Survey", , , "ngs.cors.htdp@noaa.gov", role = "cph", comment = "Author of included HTDP code") )
Maintainer: John Buonagurio <jbuonagurio@exponent.com>
Description: Provides bindings to the National Geodetic Survey (NGS) Horizontal Time Dependent Positioning (HTDP) utility, v3.2.5, written by Richard Snay, Chris Pearson, and Jarir Saleh of NGS. HTDP is a utility that allows users to transform positional coordinates across time and between spatial reference frames. See <https://www.ngs.noaa.gov/TOOLS/Htdp/Htdp.shtml> for more information.
License: MIT + file LICENSE
LazyData: TRUE
Imports: Rcpp (>= 0.12.5)
LinkingTo: Rcpp
URL: https://github.com/jbuonagurio/RHTDP
BugReports: https://github.com/jbuonagurio/RHTDP/issues
NeedsCompilation: yes
Packaged: 2016-09-19 06:32:29 UTC; jbuonagurio
Author: John Buonagurio [aut, cre], National Geodetic Survey [cph] (Author of included HTDP code)
Repository: CRAN
Date/Publication: 2016-09-19 11:06:08

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New package Tlasso with initial version 1.0.1
Package: Tlasso
Type: Package
Title: Non-Convex Optimization and Statistical Inference for Sparse Tensor Graphical Models
Version: 1.0.1
Description: An optimal alternating optimization algorithm for estimation of precision matrices of sparse tensor graphical models, and an efficient inference procedure for support recovery of the precision matrices.
Imports: huge, expm, rTensor, igraph, stats, graphics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Author: Will Wei Sun, Zhaoran Wang, Xiang Lyu, Han Liu, Guang Cheng
Maintainer: Xiang Lyu <lyu17@purdue.edu>
Depends: R (>= 3.1.1)
License: GPL (>= 2)
LazyData: true
RoxygenNote: 5.0.1
Packaged: 2016-09-19 03:27:15 UTC; alan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-09-19 07:48:04

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New package recexcavAAR with initial version 0.2.1
Package: recexcavAAR
Type: Package
Title: 3D Reconstruction of Archaeological Excavations
Version: 0.2.1
Authors@R: c( person("Clemens", "Schmid", email = "clemens@nevrome.de", role = c("cre", "cph", "aut")) )
Maintainer: Clemens Schmid <clemens@nevrome.de>
Description: A toolset for 3D reconstruction and analysis of excavations. It provides methods to reconstruct natural and artificial surfaces based on field measurements. This allows to spatially contextualize documented subunits and features. Intended to be part of a 3D visualization workflow.
Date: 2016-09-18
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
URL: https://github.com/ISAAKiel/recexcavAAR
Imports: dplyr (>= 0.4.1), plyr, magrittr (>= 1.5), reshape2 (>= 1.4.1), Rcpp, devtools
Suggests: testthat, knitr, rmarkdown, roxygen2, plotly
VignetteBuilder: knitr
Depends: R (>= 2.10), kriging (>= 1.1)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-09-18 18:20:00 UTC; clemens
Author: Clemens Schmid [cre, cph, aut]
Repository: CRAN
Date/Publication: 2016-09-19 07:48:06

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