Mon, 02 Nov 2015

New package SALTSampler with initial version 0.1
Package: SALTSampler
Type: Package
Title: Efficient Sampling on the Simplex
Version: 0.1
Date: 2015-11-01
Author: Hannah Director, Scott Vander Wiel, James Gattiker
Maintainer: Scott Vander Wiel <scottv@lanl.gov>
Imports: graphics, methods, stats
Depends: R (>= 3.0.0), lattice
Description: The SALTSampler package facilitates Monte Carlo Markov Chain (MCMC) sampling of random variables on a simplex. A Self-Adjusting Logit Transform (SALT) proposal is used so that sampling is still efficient even in difficult cases, such as those in high dimensions or with parameters that differ by orders of magnitude. Special care is also taken to maintain accuracy even when some coordinates approach 0 or 1 numerically. Diagnostic and graphic functions are included in the package, enabling easy assessment of the convergence and mixing of the chain within the constrained space.
License: BSD_3_clause + file LICENSE
Suggests: knitr, coda
VignetteBuilder: knitr
RoxygenNote: 5.0.0
NeedsCompilation: no
Packaged: 2015-11-02 00:37:21 UTC; hdirector
Repository: CRAN
Date/Publication: 2015-11-03 01:13:45

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Package MM2S updated to version 1.0.4 with previous version 1.0.3 dated 2015-08-12

Title: Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>

Diff between MM2S versions 1.0.3 dated 2015-08-12 and 1.0.4 dated 2015-11-02

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Package DLMtool updated to version 2.1.1 with previous version 2.1 dated 2015-11-01

Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>

Diff between DLMtool versions 2.1 dated 2015-11-01 and 2.1.1 dated 2015-11-02

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New package quickmapr with initial version 0.1.1
Package: quickmapr
Type: Package
Title: Quickly Map and Explore Spatial Data
Version: 0.1.1
Date: 2015-11-02
Authors@R: person(given = "Jeffrey W.",family = "Hollister", role = c("aut","cre"), email = "hollister.jeff@epa.gov")
URL: https://www.github.com/jhollist/quickmapr
BugReports: https://github.com/jhollist/quickmapr/issues
Maintainer: Jeffrey W. Hollister <hollister.jeff@epa.gov>
License: CC0
Description: While analyzing geospatial data, easy visualization is often needed that allows for quick plotting, and simple, but easy interactivity. Additionally, visualizing geospatial data in projected coordinates is also desirable. The 'quickmapr' package provides a simple method to visualize 'sp' and 'raster' objects, allows for basic zooming, panning, identifying, and labeling of spatial objects, and does not require that the data be in geographic coordinates.
Depends: R (>= 3.0.0)
Imports: rgeos, sp, rgdal, stats, grDevices, graphics, methods, httr, raster
Suggests: testthat, knitr
NeedsCompilation: no
Packaged: 2015-11-02 16:18:49 UTC; jhollist
Author: Jeffrey W. Hollister [aut, cre]
Repository: CRAN
Date/Publication: 2015-11-03 01:02:33

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Package epiDisplay updated to version 3.2.2.0 with previous version 3.2.0.6 dated 2015-07-01

Title: Epidemiological Data Display Package
Description: Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at the author's repository.
Author: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Maintainer: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>

Diff between epiDisplay versions 3.2.0.6 dated 2015-07-01 and 3.2.2.0 dated 2015-11-02

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Package rgdal updated to version 1.1-1 with previous version 1.0-7 dated 2015-09-06

Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut], Tim Keitt [aut], Barry Rowlingson [aut], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between rgdal versions 1.0-7 dated 2015-09-06 and 1.1-1 dated 2015-11-02

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Package treescape updated to version 1.8.15 with previous version 1.8.14 dated 2015-10-30

Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treescapeServer()'.
Author: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>

Diff between treescape versions 1.8.14 dated 2015-10-30 and 1.8.15 dated 2015-11-02

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New package stplanr with initial version 0.0.2
Package: stplanr
Type: Package
Title: Sustainable Transport Planning
Version: 0.0.2
Date: 2015-10-18
Authors@R: c( person("Robin", "Lovelace", email = "rob00x@gmail.com", role = c("aut", "cre")), person("Richard", "Ellison", role = c("aut"), comment = "Author of various functions"), person("Barry", "Rowlingson", role = c("aut"), comment = "Author of overline"), person("Nick", "Bearman", role = c("aut"), comment = "Co-author of gclip") )
Maintainer: Robin Lovelace <rob00x@gmail.com>
Description: Functionality and data access tools for transport planning, including origin-destination analysis, route allocation and modelling travel patterns.
License: MIT + file LICENSE
BugReports: https://github.com/ropensci/stplanr/issues
LazyData: yes
Depends: sp, R (>= 3.0)
Imports: jsonlite, maptools, raster, rgdal, rgeos, dplyr, RgoogleMaps, openxlsx, leaflet, methods, httr
Suggests: testthat, knitr, tmap
VignetteBuilder: knitr
URL: https://github.com/ropensci/stplanr
NeedsCompilation: no
Packaged: 2015-11-01 23:51:34 UTC; robin
Author: Robin Lovelace [aut, cre], Richard Ellison [aut] (Author of various functions), Barry Rowlingson [aut] (Author of overline), Nick Bearman [aut] (Co-author of gclip)
Repository: CRAN
Date/Publication: 2015-11-02 17:14:24

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Package rucm updated to version 0.5 with previous version 0.4 dated 2014-09-07

Title: Implementation of Unobserved Components Model (UCM)
Description: Unobserved Components Models (introduced in Harvey, A. (1989), Forecasting, structural time series models and the Kalman filter, Cambridge New York: Cambridge University Press) decomposes a time series into components such as trend, seasonal, cycle, and the regression effects due to predictor series which captures the salient features of the series to predict its behavior.
Author: Kaushik Roy Chowdhury
Maintainer: Kaushik Roy Chowdhury <kaushikrch@gmail.com>

Diff between rucm versions 0.4 dated 2014-09-07 and 0.5 dated 2015-11-02

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New package Rcereal with initial version 1.1.2
Package: Rcereal
Type: Package
Title: C++ Header Files of 'cereal'
Version: 1.1.2
Date: 2015-10-29
Author: Wush Wu, Randolph Voorhies, and Shane Grant
Maintainer: Wush Wu <wush978@gmail.com>
Description: To facilitate using 'cereal' with Rcpp. 'cereal' is a header-only C++11 serialization library. 'cereal' takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. 'cereal' was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
License: BSD_2_clause + file LICENSE
LazyData: TRUE
SystemRequirements: C++11
Suggests: Rcpp, git2r, httr, testthat, tools, devtools
NeedsCompilation: yes
Packaged: 2015-11-02 11:57:41 UTC; wush
Repository: CRAN
Date/Publication: 2015-11-02 18:16:53

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Package mvProbit updated to version 0.1-8 with previous version 0.1-4 dated 2015-09-03

Title: Multivariate Probit Models
Description: Tools for estimating multivariate probit models, calculating conditional and unconditional expectations, and calculating marginal effects on conditional and unconditional expectations.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between mvProbit versions 0.1-4 dated 2015-09-03 and 0.1-8 dated 2015-11-02

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Package geigen updated to version 1.8 with previous version 1.7 dated 2015-10-15

Title: Calculate Generalized Eigenvalues, the Generalized Schur Decomposition and the Generalized Singular Value Decomposition of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors, the generalized Schur decomposition and the generalized Singular Value Decomposition of a matrix pair, using Lapack routines.
Author: Berend Hasselman [cre, aut], Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>

Diff between geigen versions 1.7 dated 2015-10-15 and 1.8 dated 2015-11-02

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Package xtable updated to version 1.8-0 with previous version 1.7-4 dated 2014-09-12

Title: Export Tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables.
Author: David B. Dahl <dahl@stat.byu.edu>
Maintainer: David Scott <d.scott@auckland.ac.nz>

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Package Rcolombos updated to version 2.0.2 with previous version 1.5.3 dated 2015-09-07

Title: Interface to Colombos Compendia using the Exposed REST API
Description: Provides programmatic access to Colombos, a web based interface for exploring and analyzing comprehensive organism-specific cross-platform expression compendia of bacterial organisms.
Author: Paolo Sonego <paolo.sonego@fmach.it>
Maintainer: Paolo Sonego <paolo.sonego@fmach.it>

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Package RGoogleAnalyticsPremium updated to version 0.1.1 with previous version 0.1 dated 2015-10-29

Title: Unsampled Data in R for Google Analytics Premium Accounts
Description: It fires a query to the API to get the unsampled data in R for Google Analytics Premium Accounts. It retrieves data from the Google drive document and stores it into the local drive. The path to the excel file is returned by this package. The user can read data from the excel file into R using read.csv() function.
Author: Jalpa Joshi Dave
Maintainer: Jalpa Joshi Dave <jalpa@tatvic.com>

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Package MRIaggr updated to version 1.1.3 with previous version 1.1.2 dated 2015-05-12

Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>

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More information about MRIaggr at CRAN
Permanent link

Package metaplus updated to version 0.7-5 with previous version 0.7-4 dated 2015-07-03

Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 doi:10.1002/sim.2897 or Baker and Jackson, 2008 doi:10.1007/s10729-007-9041-8) or mixtures of normals (Beath, 2014 doi:10.1002/jrsm.1114).
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>

Diff between metaplus versions 0.7-4 dated 2015-07-03 and 0.7-5 dated 2015-11-02

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Package forestFloor updated to version 1.8.8 with previous version 1.8.6 dated 2015-09-13

Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>

Diff between forestFloor versions 1.8.6 dated 2015-09-13 and 1.8.8 dated 2015-11-02

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Package expands updated to version 1.6 with previous version 1.5 dated 2014-09-28

Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: ExPANdS characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in EXPANDS version 1.6 include: (1) So far mutations had been assigned to maximal one subpopulation. However mutations may not be exclusive to the assigned subpopulation but may also be present in smaller, descending subpopulations. This version of expands decides whether or not this is the case leveraging the predicted phylogenetic structure of the subpopulation composition. (2) Included homozygous deletion as potential scenario when modeling (SNV,CNV) pairs with overlapping genomic location, that are propagated during distinct clonal expansions. (3) Optimized solution to improve sensitivity at cell-frequency distribution margins. Need for improvement was because subpopulation detection sensitivity correlates to centrality of subpopulation size during clustering. Tolerance of copy number and allele frequency measurement errors must be higher for marginal cell-frequencies than for central cell-frequencies, in order to counteract the reduced cluster detection sensitivity at the cell-frequency distribution margins. This is only relevant during subpopulation detection (SNV clustering), cell-frequency independent error tolerance still applies during SNV assignment. (4) Fixed a bug where incorrect data matrix conversion could occur when handing non-numerical matrix as parameter to function runExPANdS. Further documentation and FAQ around ExPANdS is available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>

Diff between expands versions 1.5 dated 2014-09-28 and 1.6 dated 2015-11-02

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Package epifit updated to version 0.0.4 with previous version 0.0.3 dated 2015-10-01

Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis by a unified model specification, along with some data manipulation functions. This package covers fitting of variety models including Cox regression models, linear regression models, Poisson regression models, logistic models and others whose likelihood is expressed in negative binomial, gamma and Weibull distributions.
Author: Kazutaka Doi [aut,cre], Kei Sakabe [ctb], Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>

Diff between epifit versions 0.0.3 dated 2015-10-01 and 0.0.4 dated 2015-11-02

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