Mon, 21 Mar 2016

Package rNOMADS updated to version 2.2.0 with previous version 2.1.7 dated 2016-01-14

Title: An Interface to the NOAA Operational Model Archive and Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <danny.c.bowman@gmail.com>

Diff between rNOMADS versions 2.1.7 dated 2016-01-14 and 2.2.0 dated 2016-03-21

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 rNOMADS-2.2.0/rNOMADS/NEWS                       |    9 +
 rNOMADS-2.2.0/rNOMADS/R/GetDODS.R                |    7 
 rNOMADS-2.2.0/rNOMADS/R/RNomadsTools.R           |  179 ++++++++---------------
 rNOMADS-2.2.0/rNOMADS/man/ArchiveGribGrab.Rd     |    7 
 rNOMADS-2.2.0/rNOMADS/man/BuildProfile.Rd        |   30 ++-
 rNOMADS-2.2.0/rNOMADS/man/CheckNOMADSArchive.Rd  |    6 
 rNOMADS-2.2.0/rNOMADS/man/DODSGrab.Rd            |    2 
 rNOMADS-2.2.0/rNOMADS/man/GetClosestForecasts.Rd |   45 +++--
 rNOMADS-2.2.0/rNOMADS/man/GetDODSModelRunInfo.Rd |    3 
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 rNOMADS-2.2.0/rNOMADS/man/PlotWindProfile.Rd     |   51 ++----
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 16 files changed, 199 insertions(+), 223 deletions(-)

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New package MGGM with initial version 1.0
Package: MGGM
Type: Package
Title: Structural Pursuit Over Multiple Undirected Graphs
Version: 1.0
Suggests: MASS
Date: 2016-03-13
Author: Yunzhang Zhu, Xiaotong Shen, Wei Pan, Yiwen Sun
Maintainer: Yiwen Sun <sunxx847@umn.edu>
Description: Implement algorithms to recover multiple networks by pursuit of both sparseness and cluster.
License: GPL-2
NeedsCompilation: yes
Packaged: 2016-03-21 18:19:24 UTC; sunxx847
Repository: CRAN
Date/Publication: 2016-03-22 00:22:19

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Package EMbC updated to version 1.9.4 with previous version 1.9.3 dated 2015-07-28

Title: Expectation-Maximization Binary Clustering
Description: Unsupervised, multivariate, clustering algorithm for meaningful binary clustering and taking into account the uncertainty in the data. A specific constructor for trajectory movement analysis yields behavioural annotation of the tracks based on estimated local measures of velocity and turning angle, eventually with solar position covariate as a daytime indicator.
Author: Joan Garriga, John R.B. Palmer, Aitana Oltra, Frederic Bartumeus
Maintainer: Joan Garriga <jgarriga@ceab.csic.es>

Diff between EMbC versions 1.9.3 dated 2015-07-28 and 1.9.4 dated 2016-03-21

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Package aSPU updated to version 1.41 with previous version 1.40 dated 2016-02-18

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-single SNP association with summary statistics ('MTaSPUs').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

Diff between aSPU versions 1.40 dated 2016-02-18 and 1.41 dated 2016-03-21

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Package TwoStepCLogit updated to version 1.2.5 with previous version 1.2.4 dated 2015-12-07

Title: Conditional Logistic Regression: A Two-Step Estimation Method
Description: Conditional logistic regression with longitudinal follow up and individual-level random coefficients: A stable and efficient two-step estimation method.
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie Baillargeon
Maintainer: Thierry Duchesne <thierry.duchesne@mat.ulaval.ca>

Diff between TwoStepCLogit versions 1.2.4 dated 2015-12-07 and 1.2.5 dated 2016-03-21

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New package VSE with initial version 0.99
Package: VSE
Type: Package
Title: Variant Set Enrichment
Version: 0.99
Date: 2016-03-03
Author: Musaddeque Ahmed <musa.ahmed@utoronto.ca>
Maintainer: Hansen He <hansenhe@uhnresearch.ca>
Description: Calculates the enrichment of associated variant set (AVS) for an array of genomic regions. The AVS is the collection of disjoint LD blocks computed from a list of disease associated SNPs and their linked (LD) SNPs. VSE generates a null distribution of matched random variant sets (MRVSs) from 1000 Genome Project Phase III data that are identical to AVS, LD block by block. It then computes the enrichment of AVS intersecting with user provided genomic features (e.g., histone marks or transcription factor binding sites) compared with the null distribution.
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1.9000
Depends: GenomicRanges
Suggests: knitr, rmarkdown, ggplot2
Imports: igraph, car, IRanges, parallel
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-03-21 18:34:41 UTC; musaahmed
Repository: CRAN
Date/Publication: 2016-03-21 23:10:53

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Package mongolite updated to version 0.8.1 with previous version 0.8 dated 2016-01-23

Title: Fast and Simple MongoDB Client for R
Description: High-level, high-performance MongoDB client based on libmongoc and jsonlite. Includes support for aggregation, indexing, map-reduce, streaming, SSL encryption and SASL authentication. The vignette gives a brief overview of the available methods in the package.
Author: Jeroen Ooms [aut, cre], MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between mongolite versions 0.8 dated 2016-01-23 and 0.8.1 dated 2016-03-21

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Package MonetDB.R updated to version 1.0.1 with previous version 1.0.0 dated 2015-11-25

Title: Connect MonetDB to R
Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend.
Author: Hannes Muehleisen [aut, cre], Anthony Damico [aut], Thomas Lumley [ctb]
Maintainer: Hannes Muehleisen <hannes@cwi.nl>

Diff between MonetDB.R versions 1.0.0 dated 2015-11-25 and 1.0.1 dated 2016-03-21

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Package manifestoR updated to version 1.2 with previous version 1.1-1 dated 2015-11-12

Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from the Manifesto Corpus and to the Manifesto Project's Main Dataset and routines to analyse this data. The Manifesto Project (https://manifesto-project.wzb.eu) collects and analyses election programmes across time and space to measure the political preferences of parties. The Manifesto Corpus contains the collected and annotated election programmes in the Corpus format of the package 'tm' to enable easy use of text processing and text mining functionality. Specific functions for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre], Nicolas Merz [aut], Sven Regel [ctb], Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>

Diff between manifestoR versions 1.1-1 dated 2015-11-12 and 1.2 dated 2016-03-21

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Package Kernelheaping updated to version 1.5 with previous version 1.2 dated 2015-12-07

Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymised data the user often encounters heaped data, i.e. data which are rounded (to a possibly different degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>

Diff between Kernelheaping versions 1.2 dated 2015-12-07 and 1.5 dated 2016-03-21

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Package inbreedR updated to version 0.3.1 with previous version 0.3.0 dated 2015-11-30

Title: Analysing Inbreeding Based on Genetic Markers
Description: A framework for analysing inbreeding and heterozygosity-fitness correlations (HFCs) based on microsatellite and SNP markers.
Author: Martin A. Stoffel [aut, cre], Mareike Esser [aut], Joseph Hoffman [aut], Marty Kardos [aut]
Maintainer: Martin A. Stoffel <martin.adam.stoffel@gmail.com>

Diff between inbreedR versions 0.3.0 dated 2015-11-30 and 0.3.1 dated 2016-03-21

 DESCRIPTION                         |   23 +-
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 21 files changed, 281 insertions(+), 388 deletions(-)

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Package IMak updated to version 1.1.1 with previous version 1.1.0 dated 2016-03-03

Title: Item Maker
Description: This is an Automatic Item Generator for Psychological Testing. It is recommended for research purposes only.
Author: Diego Blum [aut, cre]
Maintainer: Diego Blum <blumworx@gmail.com>

Diff between IMak versions 1.1.0 dated 2016-03-03 and 1.1.1 dated 2016-03-21

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 7 files changed, 56 insertions(+), 56 deletions(-)

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Package htmltools updated to version 0.3.5 with previous version 0.3 dated 2015-12-29

Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>

Diff between htmltools versions 0.3 dated 2015-12-29 and 0.3.5 dated 2016-03-21

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New package ICGOR with initial version 1.0
Package: ICGOR
Type: Package
Title: Fit Generalized Odds Rate Hazards Model with Interval Censored Data
Version: 1.0
Date: 2016-03-19
Author: Jie Zhou, Jiajia Zhang, Wenbin Lu
Maintainer: Jie Zhou <zhoujie02569@gmail.com>
Description: Generalized Odds Rate Hazards (GORH) model is a flexible model of fitting survival data, including the Proportional Hazards (PH) model and the Proportional Odds (PO) Model as special cases. This package fit the GORH model with interval censored data.
License: GPL (>= 2)
Depends: R (>= 2.15.0),stats,graphics,survival,ICsurv,pracma,MASS
NeedsCompilation: no
Packaged: 2016-03-21 13:52:23 UTC; gazhou
Repository: CRAN
Date/Publication: 2016-03-21 23:35:04

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Package heavy updated to version 0.3 with previous version 0.2-35 dated 2014-09-01

Title: Robust Estimation Using Heavy-Tailed Distributions
Description: Functions to perform robust estimation considering heavy-tailed distributions. Currently, the package includes linear regression, linear mixed-effect models, multivariate location and scatter estimation, multivariate regression, penalized splines and random variate generation.
Author: Felipe Osorio
Maintainer: Felipe Osorio <felipe.osorio@ucv.cl>

Diff between heavy versions 0.2-35 dated 2014-09-01 and 0.3 dated 2016-03-21

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Package hdi updated to version 0.1-6 with previous version 0.1-5 dated 2016-03-11

Title: High-Dimensional Inference
Description: Implementation of multiple approaches to perform inference in high-dimensional models.
Author: Lukas Meier [aut, cre], Ruben Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann [aut]
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>

Diff between hdi versions 0.1-5 dated 2016-03-11 and 0.1-6 dated 2016-03-21

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New package GORCure with initial version 1.0
Package: GORCure
Type: Package
Title: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data
Version: 1.0
Date: 2016-03-07
Author: Jie Zhou, Jiajia Zhang, Wenbin Lu
Maintainer: Jie Zhou <zhoujie02569@gmail.com>
Description: Generalized Odds Rate Mixture Cure (GORMC) model is a flexible model of fitting survival data with a cure fraction, including the Proportional Hazards Mixture Cure (PHMC) model and the Proportional Odds Mixture Cure Model as special cases. This package fit the GORMC model with interval censored data.
License: GPL (>= 2)
Depends: R (>= 2.15.0),stats,graphics,survival,ICsurv,pracma,MASS
NeedsCompilation: no
Packaged: 2016-03-21 13:53:35 UTC; gazhou
Repository: CRAN
Date/Publication: 2016-03-21 22:58:51

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Package bioinactivation updated to version 1.1.2 with previous version 1.1.1 dated 2016-02-04

Title: Simulation of Dynamic Microbial Inactivation
Description: Prediction and adjustment to experimental data of microbial inactivation. Several models available in the literature are implemented.
Author: Alberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>

Diff between bioinactivation versions 1.1.1 dated 2016-02-04 and 1.1.2 dated 2016-03-21

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Package apc updated to version 1.2 with previous version 1.1 dated 2015-04-13

Title: Age-Period-Cohort Analysis
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen <bent.nielsen@nuffield.ox.ac.uk>

Diff between apc versions 1.1 dated 2015-04-13 and 1.2 dated 2016-03-21

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Package ELT updated to version 1.5 with previous version 1.4 dated 2015-09-03

Title: Experience Life Tables
Description: Build experience life tables.
Author: Julien Tomas, Frederic Planchet, Wassim Youssef
Maintainer: Wassim Youssef <Wassim.G.Youssef@gmail.com>

Diff between ELT versions 1.4 dated 2015-09-03 and 1.5 dated 2016-03-21

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Package clickstream updated to version 1.1.7 with previous version 1.1.6 dated 2016-01-08

Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e., clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>

Diff between clickstream versions 1.1.6 dated 2016-01-08 and 1.1.7 dated 2016-03-21

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