Thu, 17 Sep 2015

Package solr updated to version 0.1.6 with previous version 0.1.4 dated 2014-03-14

Title: General Purpose R Interface to Solr
Description: Provides a set of functions for querying and parsing data from Solr endpoints (local and remote), including search, faceting, highlighting, stats, and 'more like this'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between solr versions 0.1.4 dated 2014-03-14 and 0.1.6 dated 2015-09-17

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Package shinystan updated to version 2.0.1 with previous version 2.0.0 dated 2015-08-10

Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
Description: We provide a graphical user interface for interactive Markov chain Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by RStudio's Shiny web application framework and works with the output of MCMC programs written in any programming language (and has extended functionality for Stan models fit using the rstan package and the No-U-Turn sampler).
Author: Jonah Gabry [aut, cre], Stan Development Team [ctb], Michael Andreae [ctb], Michael Betancourt [ctb], Bob Carpenter [ctb], Yuanjun Gao [ctb], Andrew Gelman [ctb], Ben Goodrich [ctb], Daniel Lee [ctb], Dongying Song [ctb], Rob Trangucci [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between shinystan versions 2.0.0 dated 2015-08-10 and 2.0.1 dated 2015-09-17

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Package Rcmdr updated to version 2.2-1 with previous version 2.2-0 dated 2015-08-19

Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Milan Bouchet-Valat [aut], Liviu Andronic [ctb], Michael Ash [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter Wolf [ctb], Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package Quandl updated to version 2.7.0 with previous version 2.6.0 dated 2015-04-28

Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, downloading a zip with all data from a Quandl database, and the ability to search. This R package uses the Quandl API. For more information go to https://www.quandl.com/docs/api. For more help on the package itself go to https://www.quandl.com/help/r.
Author: Raymond McTaggart [aut, cre], Gergely Daroczi [aut], Clement Leung [aut], Quandl Inc. [cph]
Maintainer: Raymond McTaggart <raymond@quandl.com>

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Package psbcGroup updated to version 1.2 with previous version 1.1 dated 2015-02-09

Title: Penalized Semiparametric Bayesian Cox Models with Shrinkage and Grouping Priors
Description: Algorithms for fitting penalized semiparametric Bayesian Cox models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>

Diff between psbcGroup versions 1.1 dated 2015-02-09 and 1.2 dated 2015-09-17

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New package pro with initial version 0.1.1
Package: pro
Type: Package
Title: Point-Process Response Model for Optogenetics
Version: 0.1.1
Date: 2015-09-17
Author: Xi (Rossi) LUO with contributions from Dylan Small and Vikaas Sohal
Maintainer: Xi (Rossi) LUO <xi.rossi.luo@gmail.com>
Suggests: cin
Description: Optogenetics is a new tool to study neuronal circuits that have been genetically modified to allow stimulation by flashes of light. This package implements the methodological framework, Point-process Response model for Optogenetics (PRO), for analyzing data from these experiments. This method provides explicit nonlinear transformations to link the flash point-process with the spiking point-process. Such response functions can be used to provide important and interpretable scientific insights into the properties of the biophysical process that governs neural spiking in response to optogenetic stimulation.
License: GPL-2
Packaged: 2015-09-17 18:02:47 UTC; xluo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-09-17 22:50:12

More information about pro at CRAN
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Package multirich updated to version 2.1.1 with previous version 2.0.2 dated 2015-02-06

Title: Calculate Multivariate Richness via UTC and sUTC
Description: Functions to calculate Unique Trait Combinations (UTC) and scaled Unique Trait Combinations (sUTC) as measures of multivariate richness. The package can also calculate beta-diversity for trait richness and can partition this into nestedness-related and turnover components. The code will also calculate several measures of overlap.
Author: Alexander Keyel
Maintainer: Alexander Keyel <skeyel@gmail.com>

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Package laGP updated to version 1.2 with previous version 1.1-5 dated 2015-05-26

Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>

Diff between laGP versions 1.1-5 dated 2015-05-26 and 1.2 dated 2015-09-17

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Package InvariantCausalPrediction updated to version 0.3-4 with previous version 0.3-3 dated 2015-06-10

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

Diff between InvariantCausalPrediction versions 0.3-3 dated 2015-06-10 and 0.3-4 dated 2015-09-17

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Package glmmLasso updated to version 1.3.6 with previous version 1.3.5 dated 2015-08-26

Title: Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>

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Package describer updated to version 0.2.0 with previous version 0.1.0 dated 2015-09-03

Title: Describe Data in R Using Common Descriptive Statistics
Description: Allows users to quickly and easily describe data using common descriptive statistics.
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>

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Package dbscan updated to version 0.9-4 with previous version 0.9-3 dated 2015-09-03

Title: Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph], Sunil Arya [ctb, cph], David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package backtest updated to version 0.3-4 with previous version 0.3-2 dated 2013-07-09

Title: Exploring Portfolio-Based Conjectures About Financial Instruments
Description: The backtest package provides facilities for exploring portfolio-based conjectures about financial instruments (stocks, bonds, swaps, options, et cetera).
Author: Jeff Enos <jeff@kanecap.com> and David Kane <dave@kanecap.com>, with contributions from Kyle Campbell <kyle.w.campbell@williams.edu>, Daniel Gerlanc <daniel@gerlanc.com>, Aaron Schwartz <Aaron.J.Schwartz@williams.edu>, Daniel Suo <danielsuo@gmail.com>, Alexei Colin <acolin@fas.harvard.edu>, and Luyi Zhao <luyizhao@gmail.com>
Maintainer: Daniel Gerlanc <dgerlanc@enplusadvisors.com>

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Package wux updated to version 2.1-1 with previous version 2.0-2 dated 2015-06-16

Title: Wegener Center Climate Uncertainty Explorer
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik <thomas.mendlik@uni-graz.at>

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Package tsintermittent updated to version 1.7 with previous version 1.5 dated 2014-11-20

Title: Intermittent Time Series Forecasting
Description: Functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>

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Package spatialprobit updated to version 0.9-11 with previous version 0.9-10 dated 2014-05-03

Title: Spatial Probit Models
Description: Bayesian Estimation of Spatial Probit and Tobit Models.
Author: Stefan Wilhelm <wilhelm@financial.com> and Miguel Godinho de Matos <miguelgodinhomatos@cmu.edu>
Maintainer: Stefan Wilhelm <wilhelm@financial.com>

Diff between spatialprobit versions 0.9-10 dated 2014-05-03 and 0.9-11 dated 2015-09-17

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Package tmvnsim updated to version 1.0-1 with previous version 1.0-0 dated 2015-08-19

Title: Truncated Multivariate Normal Simulation
Description: Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues. Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions for multivariate normals.
Author: Samsiddhi Bhattacjarjee <sb1@nibmg.ac.in>
Maintainer: Samsiddhi Bhattacharjee <sb1@nibmg.ac.in>

Diff between tmvnsim versions 1.0-0 dated 2015-08-19 and 1.0-1 dated 2015-09-17

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Package PrevMap updated to version 1.2.3 with previous version 1.2.2 dated 2015-08-31

Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data, and is also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>

Diff between PrevMap versions 1.2.2 dated 2015-08-31 and 1.2.3 dated 2015-09-17

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New package lira with initial version 1.0
Package: lira
Type: Package
Title: LInear Regression in Astronomy
Version: 1.0
Date: 2015-09-16
Author: Mauro Sereno
Maintainer: Mauro Sereno <mauro.sereno@unibo.it>
Description: Package for Bayesian linear regression in astronomy. The method accounts for heteroscedastic errors in both the independent and the dependent variables, intrinsic scatters (in both variables), time evolution of slopes, normalization and scatters, Malmquist and Eddington bias, and break of linearity. The posterior distribution of the regression parameters is sampled with a Gibbs method exploiting the JAGS library.
License: GPL-2
Depends: R (>= 2.14.0), coda, rjags
SystemRequirements: JAGS (>= 3.0.0) (see http://mcmc-jags.sourceforge.net)
NeedsCompilation: no
Packaged: 2015-09-16 19:04:34 UTC; maurosereno
Repository: CRAN
Date/Publication: 2015-09-17 14:49:31

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New package elasso with initial version 1.0
Package: elasso
Title: Enhanced Least Absolute Shrinkage Operator
Version: 1.0
Author: Pi Guo
Maintainer: Pi Guo <guopi.01@163.com>
Description: Performs some enhanced variable selection algorithms based on least absolute shrinkage operator for regression model.
Depends: R (>= 3.0.2),glmnet,SiZer,datasets
License: GPL-2
LazyData: true
Packaged: 2015-09-17 08:30:39 UTC; Administrator
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-09-17 14:49:30

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Package VennDiagram updated to version 1.6.16 with previous version 1.6.15 dated 2015-09-09

Title: Generate High-Resolution Venn and Euler Plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>

Diff between VennDiagram versions 1.6.15 dated 2015-09-09 and 1.6.16 dated 2015-09-17

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Package vcdExtra updated to version 0.6-11 with previous version 0.6-9 dated 2015-07-11

Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package switchr updated to version 0.9.19 with previous version 0.9.18 dated 2015-09-02

Title: Installing, Managing, and Switching Between Distinct Sets of Installed Packages
Description: Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a devel/release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>

Diff between switchr versions 0.9.18 dated 2015-09-02 and 0.9.19 dated 2015-09-17

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Package spTest updated to version 0.2.1 with previous version 0.2.0 dated 2015-09-09

Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>

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Package sparr updated to version 0.3-7 with previous version 0.3-6 dated 2014-10-24

Title: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>

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Package Rlof updated to version 1.1.1 with previous version 1.1.0 dated 2015-09-11

Title: R Parallel Implementation of Local Outlier Factor(LOF)
Description: R parallel implementation of Local Outlier Factor(LOF) which uses multiple CPUs to significantly speed up the LOF computation for large datasets. (Note: The overall performance depends on the computers especially the number of the cores).It also supports multiple k values to be calculated in parallel, as well as various distance measures in addition to the default Euclidean distance.
Author: Yingsong Hu, Wayne Murray and Yin Shan, Australia.
Maintainer: Yingsong Hu <yingsonghu@hotmail.com>

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Package PSCBS updated to version 0.45.1 with previous version 0.45.0 dated 2015-09-11

Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package MIIVsem updated to version 0.4.1 with previous version 0.4 dated 2015-09-14

Title: Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
Description: Functions for estimating structural equation models using model-implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>

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Package letsR updated to version 2.3 with previous version 2.2 dated 2015-09-15

Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on species' distributions and environmental variables as well as species' description and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela <brunovilelasilva@hotmail.com>

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Package Epi updated to version 1.1.71 with previous version 1.1.67 dated 2014-07-23

Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation and manipulation of multistate data - the Lexis suite of functions, which includes interfaces to mstate, etm and cmprsk packages. Also contains functions for Age-Period-Cohort modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well some epidemiological datasets.
Author: Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Maintainer: Bendix Carstensen <bxc@steno.dk>

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Package dbmss updated to version 2.2.2 with previous version 2.2.1 dated 2015-07-14

Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>

Diff between dbmss versions 2.2.1 dated 2015-07-14 and 2.2.2 dated 2015-09-17

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 src/CountNbd.cpp     |   43 ++++++++++++++++++++++++-------------------
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