Fri, 29 Aug 2014

New package compendiumdb with initial version 0.1.0
Package: compendiumdb
Type: Package
Title: Tools for Storage and Retrieval of Gene Expession Data
Version: 0.1.0
Date: 2014-08-29
Author: Umesh Nandal , Perry D. Moerland
Maintainer: Umesh Nandal
Description: Package for the systematic collection, storage and retrieval of gene expression data via a MySQL database.
Depends: Biobase, RMySQL
Suggests: inSilicoDb, limma, hgu133a.db, GSVA, GSVAdata
SystemRequirements: Perl (>=5), MySQL (>=5.6)
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-08-29 17:20:10 UTC; ripley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-29 19:20:50

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New package iosmooth with initial version 0.91
Package: iosmooth
Type: Package
Title: Functions for smoothing with infinite order flat-top kernels
Version: 0.91
Date: 2014-08-19
Author: Timothy L. McMurry, Dimitris N. Politis
Maintainer: Timothy L. McMurry
Description: Density, spectral density, and regression estimation using infinite order kernels.
License: GPL
Packaged: 2014-08-23 18:53:39 UTC; tmcmurry
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-29 15:06:26

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Thu, 28 Aug 2014

New package Eplot with initial version 1.0
Package: Eplot
Type: Package
Title: Plotting longitudinal series
Version: 1.0
Date: 2014-08-20
Author: Eran Raviv
Maintainer: Eran Raviv
Description: Aim: Adjust the graphical parameters to create nicer longitudinal series plots. The default set of graphical parameters is very general, and can be improved upon when we are interested in plotting data points observed over time. Functions facilitate plotting those kind of series, univariate plots, bivariate plots (with vertical axis on both left and right hand sides), multivariate plots and plots which allow to examine whether a new observation is 'unusual' via construction and visualization of prediction intervals around it.
License: GPL-2
Packaged: 2014-08-28 17:06:09 UTC; MP-User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-29 01:16:24

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New package BIOM.utils with initial version 0.9
Package: BIOM.utils
Type: Package
Title: Utilities for the BIOM (Biological Observation Matrix) Format
Authors@R: person (c("Daniel", "T."), "Braithwaite", role=c("aut", "cre"), email="contact.dtb@gmail.com")
Version: 0.9
Depends: R (>= 3.0), utils
Imports:
Suggests: RJSONIO, MGRASTer
URL: https://github.com/braithwaite/BIOM.utils/
Date: 2014-08-22
Description: Provides utilities to facilitate import, export and computation with the BIOM (Biological Observation Matrix) format (http://biom-format.org).
License: BSD_2_clause + file LICENSE
Copyright: University of Chicago
LazyData: yes
Collate: source.R
Packaged: 2014-08-28 20:46:11 UTC; dan
Author: Daniel T. Braithwaite [aut, cre]
Maintainer: Daniel T. Braithwaite
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-29 01:18:59

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New package RcmdrPlugin.FactoMineR with initial version 1.5-0
Package: RcmdrPlugin.FactoMineR
Type: Package
Version: 1.5-0
Date: 2014-08-12
Title: Graphical User Interface for FactoMineR
Author: Francois Husson, Julie Josse, Sebastien Le
Maintainer: Francois Husson
Imports: Rcmdr (>= 2.0-0), tcltk
Depends: FactoMineR
Description: Rcmdr Plugin for the FactoMineR package
License: GPL (>= 2)
URL: http://factominer.free.fr, http://www.agrocampus-ouest.fr/math/
LazyLoad: no
Encoding: latin1
Packaged: 2014-08-28 19:10:16 UTC; husson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-29 01:11:08

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New package bvarsv with initial version 1.0
Package: bvarsv
Type: Package
Title: Bayesian Analysis of a Vector Autoregressive Model with Stochastic Volatility and Time-Varying Parameters
Version: 1.0
Date: 2014-08-22
Author: Fabian Krueger
Maintainer: Fabian Krueger
Description: R/C++ implementation of the model proposed by Primiceri ("Time Varying Structural Vector Autoregressions and Monetary Policy", Review of Economic Studies, 2005), with a focus on generating posterior predictive distributions.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp, RcppArmadillo
URL: https://sites.google.com/site/fk83research/code
Packaged: 2014-08-28 11:37:09 UTC; kruegefn
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-28 19:56:22

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New package NPBayesImpute with initial version 0.1
Package: NPBayesImpute
Type: Package
Title: Non-parametric Bayesian Multiple Imputation for Categorical Data
Version: 0.1
Date: 2014-04-05
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Quanli Wang
Description: These routines create multiple imputations of missing at random categorical data, with or without structural zeros. Imputations are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
License: GPL (>= 3)
Depends: methods, Rcpp (>= 0.10.2)
LinkingTo: Rcpp
RcppModules: clcm
Packaged: 2014-08-28 12:51:41 UTC; quanli
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-28 15:12:18

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New package parsedate with initial version 1.0.2
Package: parsedate
Title: Recognize and parse dates in various formats, including all ISO 8601 formats
Version: 1.0.2
Maintainer: Gabor Csardi
Author: Gabor Csardi, Linus Torvalds
Description: Parse dates automatically, without the need of specifying a format. Currently it includes the git date parser. It can also recognize and parse all ISO 8601 formats.
License: GPL-2
LazyData: true
Depends: methods
Imports: lubridate
Suggests: testthat
URL: https://github.com/gaborcsardi/parsedate
BugReports: https://github.com/gaborcsardi/parsedate/issues
Packaged: 2014-08-28 10:58:49 UTC; gaborcsardi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-28 13:12:40

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Wed, 27 Aug 2014

New package trajectories with initial version 0.1-0
Package: trajectories
Version: 0.1-0
Date: 2014-08-27
Title: Classes and methods for trajectory data
Authors@R: c(person("Edzer", "Pebesma", role = c("cre", "aut"), email = "edzer.pebesma@uni-muenster.de"), person("Benedikt", "Klus", role = "aut"))
Depends: R (>= 2.14.0)
Imports: methods, lattice, sp (>= 1.0-14), spacetime (>= 1.0-0), rgdal, rgeos
Suggests: rgl, OpenStreetMap, RCurl, rjson, adehabitatLT
LazyData: no
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
License: GPL (>= 2)
URL: http://github.com/edzer/trajectories
Collate: Class-Tracks.R Tracks-methods.R stplot.R
Packaged: 2014-08-27 21:05:41 UTC; edzer
Author: Edzer Pebesma [cre, aut], Benedikt Klus [aut]
Maintainer: Edzer Pebesma
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-28 00:05:09

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New package replicationInterval with initial version 0.1
Package: replicationInterval
Type: Package
Title: Replication Interval Functions
Version: 0.1
Date: 2014-08-27
Author: David Stanley
Maintainer: David Stanley
Description: A common problem faced by journal reviewers and authors is the question of whether the results of a replication study are consistent with the original published study. One solution to this problem is to examine the effect size from the published study and generate the range of effect sizes that could reasonably be obtained (due to random sampling) in a replication attempt (i.e., calculate a replication interval). If a replication effect size falls outside the replication interval then that value could not have occurred to due the effects of sampling error alone. Alternatively, if a replication effect size falls within the replication interval then the replication results could have reasonably occurred due to the effects of sampling error alone. This package has functions that calculate the replication interval for two different types of effect sizes (i.e., correlation, Cohen's d).
Imports: MBESS
License: Unlimited
Packaged: 2014-08-27 20:23:22 UTC; stanley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 23:32:23

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New package dotenv with initial version 1.0
Package: dotenv
Title: Load environment variables from .env
Version: 1.0
Authors@R: "Gabor Csardi [aut, cre]"
Description: Load configuration from a .env file, that is in the current working directory, into environment variables.
License: MIT + file LICENSE
LazyData: true
Imports: magrittr, falsy
URL: https://github.com/gaborcsardi/dotenv
BugReports: https://github.com/gaborcsardi/dotenv/issues
Packaged: 2014-08-27 19:55:50 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 23:42:52

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New package lmeVarComp with initial version 1.0
Package: lmeVarComp
Type: Package
Title: Testing for a subset of variance components in linear mixed models
Version: 1.0
Date: 2014-08-27
Author: Yichi Zhang
Maintainer: Yichi Zhang
Description: Test zero variance components in linear mixed models and test additivity in nonparametric regression using the restricted likelihood ratio test and the generalized F-test.
License: GPL (>= 2)
Suggests: RLRsim, varComp
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2014-08-27 17:33:32 UTC; yzhang52
Repository: CRAN
Date/Publication: 2014-08-27 21:17:18

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New package shopifyr with initial version 0.28
Package: shopifyr
Type: Package
Title: An R Interface to the Shopify API
Version: 0.28
Date: 2014-07-28
Author: Charlie Friedemann
Maintainer: Charlie Friedemann
Description: An interface to the API of the E-commerce service Shopify (http://docs.shopify.com/api)
URL: https://github.com/charliebone/shopifyr/
License: GPL-3
Depends: R (>= 3.0), RCurl
Imports: R6 (>= 2.0), RJSONIO
Collate: 'Announcement.R' 'ApplicationCharge.R' 'Article.R' 'Asset.R' 'Blog.R' 'CarrierService.R' 'Checkout.R' 'Collect.R' 'Comment.R' 'Country.R' 'CustomCollection.R' 'Customer.R' 'CustomerGroup.R' 'Event.R' 'Fulfillment.R' 'FulfillmentService.R' 'Location.R' 'MetaField.R' 'Order.R' 'OrderRisks.R' 'Page.R' 'Product.R' 'ProductImage.R' 'ProductVariant.R' 'Province.R' 'RecurringApplicationCharge.R' 'Redirect.R' 'Refund.R' 'ScriptTag.R' 'Shop.R' 'private.R' 'Webhook.R' 'Transaction.R' 'Theme.R' 'SmartCollection.R' 'ShopifyShop.R' 'shopfyr-package.R'
Packaged: 2014-08-27 15:24:00 UTC; Charlie
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 18:04:04

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New package falsy with initial version 1.0
Package: falsy
Title: Define truthy and falsy values
Version: 1.0
Authors@R: "Gabor Csardi [aut, cre]"
Description: A value is falsy if it is NULL, FALSE, the empty string, zero, or an empty vector or list. Other values are truthy. The new %&&% and %||% operators work with falsy and truthy values and can be used for concise conditional execution.
License: MIT + file LICENSE
Suggests: testthat
URL: https://github.com/gaborcsardi/falsy
BugReports: https://github.com/gaborcsardi/falsy/issues
Packaged: 2014-08-27 16:10:35 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 18:52:29

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New package decompr with initial version 1.1
Package: decompr
Type: Package
Title: Export Decomposition (Wang-Wei-Zhu and source)
Version: 1.1
Date: 2014-08-27
Author: Bastiaan Quast
Maintainer: Bastiaan Quast
Description: The R package 'decompr' implements two export decomposition algorithms. Firstly, the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross exports into 16 value added components. Secondly, the Source decomposition algorithm derives the value added origin of exports by country and industry, which is also based on Wang, Wei, and Zhu (2013).
Depends: R (>= 2.10)
License: GPL-3
Packaged: 2014-08-27 13:03:19 UTC; quast2
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 18:09:17

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New package Crossover with initial version 0.1-10
Package: Crossover
Type: Package
Title: Crossover Designs
Version: 0.1-10
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer
Description: Package Crossover provides different crossover designs from combinatorial or search algorithms as well as from literature and a GUI to access them.
Depends: R (>= 3.0.2), rJava (>= 0.8-3), CommonJavaJars (>= 1.0.5), JavaGD, ggplot2
Imports: MASS, crossdes (>= 1.1-1), xtable, methods, Matrix, multcomp, stats4, digest
Suggests: knitr, RUnit, nlme
SystemRequirements: Java (>= 5.0)
LinkingTo: Rcpp (>= 0.10.3), RcppArmadillo (>= 0.2.0)
License: GPL-2
VignetteBuilder: knitr
URL: https://github.com/kornl/Crossover/wiki
BugReports: https://github.com/kornl/Crossover/issues
Packaged: 2014-08-27 14:36:10 UTC; kornel
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-27 17:28:51

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New package statebins with initial version 1.0
Package: statebins
Type: Package
Title: statebins is an alternative to choropleth maps for USA States
Version: 1.0
Date: 2014-08-26
Author: Bob Rudis (@hrbrmstr)
Maintainer: Bob Rudis
Description: statebins is an alternative to choropleth maps for USA States and is based on work by the Washington Post graphics department in their report on "The states most threatened by trade". statebins preserves as much of the geographic placement of the states as possible but has the look and feel of a traditional heatmap. Functions are provided that allow for use of both a binned, discrete scale and continuous scale depending on what is needed for the underlying data.
URL: http://github.com/hrbrmstr/statebins
BugReports: https://github.com/hrbrmstr/statebins/issues
License: MIT + file LICENSE
Suggests: testthat
Depends: R (>= 3.0.0), ggplot2, grid, scales, gridExtra, RColorBrewer
Packaged: 2014-08-27 13:24:41 UTC; bob
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 16:35:46

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New package SelvarMix with initial version 1.0
Package: SelvarMix
Type: Package
Title: Regularization for variable selection in model-based clustering and discriminant analysis.
Version: 1.0
Date: 2014-04-03
Author: Mohammed Sedki, Gilles Celeux, Cathy Maugis-Rabusseau
Maintainer: Mohammed Sedki
Description: Regularization for variable selection in model-based clustering and discriminant analysis
License: GPL (>= 3)
Imports: Rcpp (>= 0.11.1), glasso, parallel, Rmixmod
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2014-08-27 08:54:54 UTC; sedki
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-27 11:13:29

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New package rsdmx with initial version 0.3
Package: rsdmx
Version: 0.3
Date: 2014-08-27
Title: A package to read SDMX data and metadata
Authors@R: c( person("Emmanuel", "Blondel", role = c("aut", "cre"), email = "emmanuel.blondel1@gmail.com"), person("Matthieu", "Stigler", role = c("ctb")))
Maintainer: Emmanuel Blondel
Depends: R (>= 2.15)
Imports: methods, XML (>= 3.96-1.1), RCurl, plyr
Suggests: testthat
Description: The package hosts a set of classes and methods to parse/read SDMX data and metadata.
License: GPL (>= 2)
URL: https://github.com/opensdmx/rsdmx
BugReports: https://github.com/opensdmx/rsdmx/issues
LazyLoad: yes
Collate: Class-SDMXSchema.R Class-SDMXType.R Class-SDMXStructureType.R Class-SDMXHeader.R Class-SDMX.R Class-SDMXGenericData.R Class-SDMXCompactData.R Class-SDMXMessageGroup.R Class-SDMXConcept.R Class-SDMXConceptScheme.R Class-SDMXConcepts.R Class-SDMXCode.R Class-SDMXCodelist.R Class-SDMXCodelists.R Class-SDMXDimension.R Class-SDMXTimeDimension.R Class-SDMXPrimaryMeasure.R Class-SDMXAttribute.R Class-SDMXComponents.R Class-SDMXDataStructure.R Class-SDMXDataStructures.R Class-SDMXDataStructureDefinition.R SDMXSchema-methods.R SDMXType-methods.R SDMXStructureType-methods.R SDMXHeader-methods.R SDMX-methods.R SDMXGenericData-methods.R SDMXCompactData-methods.R SDMXMessageGroup-methods.R SDMXConcept-methods.R SDMXConceptScheme-methods.R SDMXConcepts-methods.R SDMXCode-methods.R SDMXCodelist-methods.R SDMXCodelists-methods.R SDMXDimension-methods.R SDMXTimeDimension-methods.R SDMXPrimaryMeasure-methods.R SDMXAttribute-methods.R SDMXComponents-methods.R SDMXDataStructure-methods.R SDMXDataStructures-methods.R SDMXDataStructureDefinition-methods.R readSDMX.R
Packaged: 2014-08-27 08:54:13 UTC; Utilisateur
Author: Emmanuel Blondel [aut, cre], Matthieu Stigler [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 11:13:31

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Tue, 26 Aug 2014

New package rucm with initial version 0.3
Package: rucm
Type: Package
Title: Implementation of Unobserved Components Model (UCM) in R
Version: 0.3
Date: 2014-08-25
Author: Kaushik Roy Chowdhury
Maintainer: Kaushik Roy Chowdhury
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.
License: GPL (>= 2)
Depends: KFAS
Packaged: 2014-08-25 09:54:52 UTC; k.roy.chowdhury
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-26 22:55:16

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New package cents with initial version 0.1-41
Package: cents
Version: 0.1-41
Date: 2014-08-26
Title: Censored time series
Author: A.I. McLeod, Nagham M. Mohammad, Justin Veenstra and Abdel El-Shaarawi
Maintainer: A.I. McLeod
Depends: R (>= 2.1.0)
Description: Fit censored time series
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
Packaged: 2014-08-26 16:26:32 UTC; IanMcLeod
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-26 22:14:53

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New package TR8 with initial version 0.8
Package: TR8
Type: Package
Title: A tool for downloading functional traits data for plant species
Version: 0.8
Date: 2014-02-27
Author: Gionata Bocci
Maintainer: Gionata Bocci
Description: Plant ecologists often need to collect "traits" data about plant species which are often scattered among various databases: TR8 contains a set of tools which take care of automatically retrieving some of those functional traits data for plant species from publicly available databases (Biolflor, The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity database). The TR8 name, inspired by "car plates" jokes, was chosen since it both reminds of the main object of the package and is extremely short to type.
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
Depends: R (>= 2.10), XML, RCurl, plyr, methods, taxize
Imports: gWidgets
Packaged: 2014-08-26 14:27:39 UTC; gionata
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-26 18:17:06

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New package sparseSEM with initial version 2.3
Package: sparseSEM
Type: Package
Title: Sparse-aware Maximum Likelihood for Structural Equation Models
Version: 2.3
Date: 2013-08-28
Author: Anhui Huang; Xiaodong Cai
Maintainer: Anhui Huang
Description: Sparse-aware maximum likelihood for structural equation models in inferring gene regulatory networks
License: GPL
Packaged: 2014-08-26 12:04:23 UTC; Anhui
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-26 15:41:43

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New package ENMeval with initial version 0.1.0
Package: ENMeval
Type: Package
Title: Automated runs and evaluations of ecological niche models
Version: 0.1.0
Date: 2014-08-25
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006).
License: GPL
Depends: dismo, raster, rJava (>= 0.5-0), methods, R (>= 2.10)
Packaged: 2014-08-25 23:15:54 UTC; Bob
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-26 07:52:35

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New package DepthProc with initial version 1.0.1
Package: DepthProc
Version: 1.0.1
Date: 2014-08-18
Title: DepthProc
Author: Daniel Kosiorowski, Mateusz Bocian, Anna Wegrzynkiewicz and Zygmunt Zawadzki from Cracow University of Economics.
Maintainer: Zygmunt Zawadzki
Description: Package for depths
License: GPL-2
Depends: R (>= 3.0.0), ggplot2, Rcpp (>= 0.11.2), rrcov, np, methods, MASS
Imports: lattice, sm, geometry
Suggests: mvtnorm, rgl, sn, robustbase,
LinkingTo: Rcpp, RcppArmadillo
Repository: CRAN
Repository/R-Forge/Project: depthproc
Repository/R-Forge/Revision: 56
Repository/R-Forge/DateTimeStamp: 2014-08-25 14:10:36
Date/Publication: 2014-08-26 07:56:08
Packaged: 2014-08-26 05:33:43 UTC; ripley
NeedsCompilation: yes

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New package BTSPAS with initial version 2014.0901
Package: BTSPAS
Version: 2014.0901
Date: 2014-09-01
Title: Bayesian Time-Strat. Population Analysis
Author: Carl J Schwarz and Simon J Bonner
Maintainer: Carl J Schwarz
Imports: coda, splines, actuar, rjags, R2OpenBUGS, ggplot2, plyr
Suggests: BRugs
SystemRequirements: JAGS
Description: BTSPAS provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments. Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size. This version uses JAGS to sample from the posterior distribution.
License: GPL (>= 2)
URL: http://www.stat.sfu.ca/~cschwarz/Consulting/Trinity/Phase2
Packaged: 2014-08-25 23:42:16 UTC; cschwarz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-26 07:51:36

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Mon, 25 Aug 2014

New package testthatsomemore with initial version 0.1
Package: testthatsomemore
Title: A mocking, stubbing, and file testing framework extending testthat
Version: 0.1
Maintainer: Robert Krzyzanowski
Authors@R: c(person("Robert", "Krzyzanowski", email = "technoguyrob@gmail.com", role = c("aut", "cre")))
Description: This package intends to go above and beyond of the features provided by the testthat package. Namely, stubbing of functions and methods is provided as well as the ability to architect mock structured hierarchies of files (sometimes called fixtures). Intended for developers, testthatsomemore aims to raise the caliber of R testing frameworks to that of famous libraries like JUnit and RSpec.
Depends: R (>= 3.0.0)
Imports: testthat
License: MIT + file LICENSE
LazyData: true
URL: http://github.com/robertzk/testthatsomemore
Packaged: 2014-08-24 09:23:00 UTC; robertk
Author: Robert Krzyzanowski [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-26 00:21:39

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New package sns with initial version 0.9
Package: sns
Type: Package
Title: Stochastic Newton Sampler
Version: 0.9
Date: 2014-8-25
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.S. Sharabiani
Maintainer: Asad Hasan
Description: Multivariate, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability densities. SNS is a Metropolis-Hastings variant, with a special form of the proposal function. The proposal function is a local Gaussian approximation to the density obtained via Taylor expansion of the log-density around the current point. The mean of the Gaussian proposal is taken as the full Newton-Raphson step from the current point. During burn-in, Newton-Raphson optimization is performed to get close to the mode of the pdf which is unique due to convexity.
License: GPL (>= 2)
Imports: mvtnorm
Packaged: 2014-08-25 20:13:37 UTC; ahasan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-25 22:26:38

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New package remote with initial version 0.3.0
Package: remote
Type: Package
Title: Empirical Orthogonal Teleconnections in R
Version: 0.3.0
Date: 2014-08-25
Author: Tim Appelhans, Florian Detsch, Thomas Nauss
Maintainer: Tim Appelhans
Description: 'remote' is short for "R(-based) EMpirical Orthogonal TEleconnections". It implements a collection of functions to facilitate empirical orthogonal teleconnection analysis. Empirical Orthogonal Teleconnections (EOTs) denote a regression based approach to decompose spatio-temporal fields into a set of independent orthogonal patterns. They are quite similar to Empirical Orthogonal Functions (EOFs) with EOTs producing less abstract results. In contrast to EOFs, which are orthogonal in both space and time, EOT analysis produces patterns that are orthogonal in either space or time.
License: GPL (>= 3) | file LICENSE
Depends: R (>= 2.10), Rcpp (>= 0.10.3), raster, foreach, methods
Suggests: maps, lattice, latticeExtra, grid, gridExtra, sp
LinkingTo: Rcpp
Packaged: 2014-08-25 09:55:01 UTC; ede
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-25 16:03:36

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New package boral with initial version 0.4
Package: boral
Title: Bayesian Ordination and Regression AnaLysis
Version: 0.4
Date: 2014-05-06
Author: Francis K.C. Hui
Maintainer: Francis Hui
Description: Bayesian model-based approaches for analyzing multivariate data in ecology. Estimation is performed using Bayesian/Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs such that the columns of the response matrix are assumed to be independent; 2) With latent variables only, boral fits a purely latent variable model to perform model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
License: GPL-2
Depends: coda
Imports: R2jags, mvtnorm, fishMod, MASS
Suggests: mvabund (>= 3.8.4), corrplot
NeedsCompilation: no
Packaged: 2014-08-25 12:59:22 UTC; fhui
Repository: CRAN
Date/Publication: 2014-08-25 16:03:32

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New package MultNonParam with initial version 1.0
Package: MultNonParam
Type: Package
Title: Multivariate Nonparametric Methods
Version: 1.0
Date: 2014-08-21
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and somealgorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
License: GPL-2
Packaged: 2014-08-21 19:16:11 UTC; kolassa
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-25 08:10:42

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Sun, 24 Aug 2014

New package dunn.test with initial version 1.1.0
Package: dunn.test
Version: 1.1.0
Date: 2014-08-23
Title: Dunn's test of multiple comparisons using rank sums
Author: Alexis Dinno
Maintainer: Alexis Dinno
Description: dunn.test computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
License: GPL-2
LazyData: no
Encoding: UTF-8
Packaged: 2014-08-24 22:12:01 UTC; Alexis
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-25 01:00:40

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New package CosmoPhotoz with initial version 0.1
Package: CosmoPhotoz
Type: Package
Title: Photometric redshift estimation using generalized linear models
Version: 0.1
Date: 2014-08-20
Author: Rafael S. de Souza, Alberto Krone-Martins, Jonathan Elliott, Joseph Hilbe
Maintainer: Rafael S. de Souza
Description: User-friendly interfaces to perform fast and reliable photometric redshift estimation. The code makes use of generalized linear models and can adopt gamma or inverse gaussian families, either from a frequentist or a Bayesian perspective. The code additionally provides a Shiny application providing a simple user interface.
Depends: R (>= 3.0)
License: GPL (>= 3)
Imports: ggplot2, ggthemes, arm, COUNT, gridExtra, pcaPP, mvtnorm, shiny
NeedsCompilation: no
Packaged: 2014-08-23 22:48:52 UTC; rafael
Repository: CRAN
Date/Publication: 2014-08-24 07:22:40

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Sat, 23 Aug 2014

New package sonicLength with initial version 1.4.4
Package: sonicLength
Type: Package
Title: Estimating Abundance of Clones from DNA fragmentation data
Version: 1.4.4
Date: 2014-08-23
Author: Charles Berry
Maintainer: Charles Berry
Depends: R (>= 2.14.0), splines
Description: Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.
License: GPL (>= 2)
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: soniclength
Repository/R-Forge/Revision: 8
Repository/R-Forge/DateTimeStamp: 2014-08-23 15:50:30
Date/Publication: 2014-08-24 00:23:07
Packaged: 2014-08-23 16:15:22 UTC; rforge
NeedsCompilation: no

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New package preseqR with initial version 1.0
Package: preseqR
Type: Package
Title: Predicting Species Accumulation
Version: 1.0
Date: 2014-08-23
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng
Description: Estimating species accumulation curves by rational function approximations to the non-parametric empirical Bayes estimator and by the zero-truncated Negative Binomial distribution.
License: GPL-3
Packaged: 2014-08-23 19:40:28 UTC; jake
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-24 00:41:57

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New package mkde with initial version 0.1
Package: mkde
Type: Package
Title: 2D and 3D movement-based kernel density estimates (MKDEs).
Version: 0.1
Date: 2011-08-23
Author: Jeff A. Tracey, James Sheppard, Jun Zhu, Robert Sinkovts, Amit Chourasia, Glenn Lockwood, and Robert N. Fisher
Maintainer: Jeff A. Tracey
Description: Provides functions to compute and visualize movement-based kernel density estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimensions.
License: GPL (>= 3)
LazyLoad: yes
Depends: R (>= 2.10)
Imports: Rcpp (>= 0.9.6), raster, sp
LinkingTo: Rcpp
Packaged: 2014-08-23 20:26:48 UTC; jeff
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-24 00:26:36

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New package unittest with initial version 1.0-0
Encoding: UTF-8
Package: unittest
Type: Package
Title: TAP-compliant unit testing.
Version: 1.0-0
Date: 2014-08-23
Authors@R: c(person('Jamie','Lentin',email='jm@ravingmantis.com',role=c('aut')), person('Anthony','Hennessey',email='ah@ravingmantis.com',role=c('aut','cre')))
Description: Concise TAP (http://testanything.org/) compliant unit testing package. Produces tests that can be run with CMD check with minimal implementation overhead.
License: GPL (>= 3)
Depends: R (>= 3.0.0)
Imports:
Suggests:
BugReports: https://github.com/ravingmantis/unittest/issues
LazyData: yes
Packaged: 2014-08-23 12:50:38 UTC; albert
Author: Jamie Lentin [aut], Anthony Hennessey [aut, cre]
Maintainer: Anthony Hennessey
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-23 19:42:45

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New package CompRandFld with initial version 1.0.3-1
Package: CompRandFld
Version: 1.0.3-1
Date: 2014-08-22
Title: Composite-likelihood based Analysis of Random Fields
Author: Simone Padoan , Moreno Bevilacqua
Maintainer: Simone Padoan
Depends: R (>= 2.12.0)
Description: The aim of this package is to collect a set of procedures for the analysis of Random Fields by Composite Likelihood methods. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood based methods are emerging as useful tools for mitigating such computational problems and show satisfactory results when compared with other techniques such as, for example the tapering method. Moreover, composite likelihood (and related quantities) have some good properties similar to those of the standard likelihood.
Suggests: RandomFields, spam, scatterplot3d, fields, mapproj
License: GPL (>= 2)
URL: http://faculty.unibocconi.it/simonepadoan
Repository: CRAN
Packaged: 2014-08-23 08:36:31 UTC; Padoan
NeedsCompilation: yes
Date/Publication: 2014-08-23 10:49:57

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New package bigRR with initial version 1.3-10
Package: bigRR
Type: Package
Title: Generalized Ridge Regression (with special advantage for p >> n cases)
Version: 1.3-10
Date: 2014-08-23
Author: Xia Shen, Moudud Alam and Lars Ronnegard
Maintainer: Xia Shen
Description: The package fits large-scale (generalized) ridge regression for various distributions of response. The shrinkage parameters (lambdas) can be pre-specified or estimated using an internal update routine (fitting a heteroscedastic effects model, or HEM). It gives possibility to shrink any subset of parameters in the model. It has special computational advantage for the cases when the number of shrinkage parameters exceeds the number of observations. For example, the package is very useful for fitting large-scale omics data, such as high-throughput genotype data (genomics), gene expression data (transcriptomics), metabolomics data, etc.
Depends: R (>= 2.10), utils, hglm, DatABEL
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-08-23 06:09:24 UTC; xia
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-23 09:38:31

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New package pauwels2014 with initial version 1.0
Package: pauwels2014
Type: Package
Title: Bayesian Experimental Design for Systems Biology.
Version: 1.0
Date: 2014-08-20
Author: Edouard Pauwels
Maintainer: Edouard Pauwels
Description: Implementation of a Bayesian active learning strategy to carry out sequential experimental design in the context of biochemical network kinetic parameter estimation. This package gathers functions and pre-computed data sets to reproduce results presented in Pauwels E. et. al published in BMC Systems Biology, 2014. Scripts are given to compute all results from scratch or to draw pictures based on pre-computed data sets.
License: GPL-3
Depends: deSolve, ggplot2, R (>= 2.10)
NeedsCompilation: yes
Packaged: 2014-08-22 16:32:19 UTC; ed
Repository: CRAN
Date/Publication: 2014-08-23 08:12:04

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New package mppa with initial version 1.0
Package: mppa
Type: Package
Title: Statistics for analysing multiple simultaneous point processes on the real line
Version: 1.0
Date: 2014-08-16
Author: Patrick Rubin-Delanchy and Nicholas A Heard
Maintainer: Patrick Rubin-Delanchy
Description: A procedure to test for dependence between point processes on the real line, e.g. causal dependence, correlation, inhibition or anti-correlation. The package also provides a number of utilities for plotting simultaneous point processes, and combining p-values.
License: GPL (>= 2)
Depends: R (>= 2.2.0), methods, stats
Packaged: 2014-08-22 23:05:17 UTC; patrick
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-23 08:06:06

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Fri, 22 Aug 2014

New package survAccuracyMeasures with initial version 1.2
Package: survAccuracyMeasures
Type: Package
Title: Estimate accuracy measures for risk prediction markers from survival data
Version: 1.2
Date: 2014-08-22
Author: Yingye Zheng, Tianxi Cai, and Marshall Brown
Maintainer: Marshall Brown
Description: This package provides a function to estimate the AUC, TPR(c), FPR(c), PPV(c), and NPV(c) for for a specific timepoint and marker cutoff value c using non-parametric and semi-parametric estimators. Standard errors and confidence intervals are also computed. Either analytic or bootstrap standard errors can be computed.
License: GPL-2
Depends: survival, splines
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
URL: https://github.com/mdbrown/survRpackages
Packaged: 2014-08-22 20:40:15 UTC; mdbrown
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-23 00:46:22

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New package NHANES with initial version 1.0
Package: NHANES
Type: Package
Title: NHANES data
Version: 1.0
Date: 2014-08-21
Author: Randall Pruim , Daniel Kaplan , Nicholas Horton
Maintainer: Randall Pruim
Description: Body Shape and related measurements from the US National Health and Nutrition Examination Survey (NHANES, 1999-2004). See http://www.cdc.gov/nchs/nhanes.htm for details.
License: GPL (>= 2)
Depends: R (>= 3.0.0)
LazyLoad: yes
LazyData: yes
Packaged: 2014-08-22 20:29:35 UTC; rpruim
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-23 00:51:01

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New package mosaicData with initial version 0.9.1
Package: mosaicData
Type: Package
Title: Project MOSAIC (mosaic-web.org) data sets
Version: 0.9.1
Date: 2014-08-21
Depends: R (>= 3.0.0)
Suggests: lattice, mosaic, reshape2
Author: Randall Pruim , Daniel Kaplan , Nicholas Horton
Maintainer: Randall Pruim
Description: Data sets from Project MOSAIC (mosaic-web.org) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2014-08-22 20:53:42 UTC; rpruim
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-23 01:02:56

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Thu, 21 Aug 2014

New package childsds with initial version 0.5
Package: childsds
Title: Calculation of standard deviation scores adduced from different growth standards
Version: 0.5
Authors@R: c(person("Mandy", "Vogel", role=c("aut","cre"), email="mandy.vogel@medizin.uni-leipzig.de"))
Description: Calculation of standard deviation scores from different growth standards
Depends: R (>= 3.1.1), methods
License: GPL (>= 2)
LazyData: true
Packaged: 2014-08-21 17:06:37 UTC; mvogel
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-21 19:22:42

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New package sensory with initial version 1.0
Package: sensory
Type: Package
Title: Simultaneous Model-Based Clustering and Imputation via a Progressive Expectation-Maximization (PEM) algorithm.
Version: 1.0
Date: 2014-08-20
Author: Brian C. Franczak, Ryan P. Browne and Paul D. McNicholas
Maintainer: Brian C. Franczak
Description: Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously.
Depends: Matrix, gtools, MASS, R (>= 3.1.1)
NeedsCompilation: no
License: GPL (>= 2)
Packaged: 2014-08-21 15:59:51 UTC; brianfranczak
Repository: CRAN
Date/Publication: 2014-08-21 18:36:52

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New package RAM with initial version 1.0.0
Package: RAM
Type: Package
Title: R for Amplicon-based Metagenomics
Version: 1.0.0
Date: 2014-08-20
Author: Wen Chen and Joshua Simpson
Copyright: Government of Canada
Maintainer: Wen Chen
Description: This package provides a series of functions to make amplicon-based metagenomic analysis more accessible, and publication-quality plots simple. Amplicon-based (or targeted) metagenomics amplifies and sequences selected DNA regions of environmental samples, but not the entire pool of genetic material, which is referred to as shotgun metagenomics. The amplicon-metagenomics mainly aims at characterizing broad microbiota biodiversity in different environments.
License: MIT + file LICENSE
Depends: vegan, ggplot2, stats
Imports: gridExtra, RColorBrewer, indicspecies, Heatplus, splitstackshape, gplots, plyr, reshape2, scales, labdsv, grid, stringr, ggmap, permute
Suggests: testthat
Packaged: 2014-08-21 14:34:51 UTC; chenw
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-21 19:00:07

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New package SparseTSCGM with initial version 2.1.1
Package: SparseTSCGM
Type: Package
Title: Sparse time series chain graphical models
Version: 2.1.1
Date: 2014-04-15
Depends: R(>= 3.0.2)
Imports: glasso, longitudinal, flare, MASS, mvtnorm, network, abind
Author: Fentaw Abegaz and Ernst Wit
Maintainer: Fentaw Abegaz
Description: Computes sparse vector autoregressive coefficients and precision matrices for time series chain graphical models.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2014-08-20 14:47:44 UTC; p261204
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-21 06:43:12

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Wed, 20 Aug 2014

New package geoBayes with initial version 0.1.2
Package: geoBayes
Type: Package
Title: Analysis of geostatistical data using Bayes and Empirical Bayes methods
Description: This package provides functions to fit geostatistical data. The data can be continuous, binary or count data and the models implemented are flexible. Conjugate priors are assumed on some parameters while non-conjugate parameters can be estimated either by Monte-Carlo or empirical Bayes methods.
Version: 0.1.2
Date: 2014-08-20
Author: Evangelos Evangelou , Vivekanda Roy
Maintainer: Evangelos Evangelou
Imports: stats, coda, sp
Depends: R (>= 2.0.0)
Suggests: geoR, geoRglm
LazyData: true
License: GPL (>= 2)
Classification/ACM: 86A32, 62M30, 62F15
Packaged: 2014-08-20 18:16:16 UTC; ee224
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-20 21:07:01

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New package metaplus with initial version 0.6-0
Package: metaplus
Type: Package
Title: Robust meta-analysis and meta-regression.
Version: 0.6-0
Date: 2014-08-20
Author: Ken Beath
Maintainer: Ken Beath
Description: Performs meta-analysis using standard and robust methods with confidence intervals from profile likelihood.
Depends: R(>= 3.1.0), bbmle, metafor
Imports: boot, methods, numDeriv
License: GPL (>= 2)
Packaged: 2014-08-20 09:08:57 UTC; kjbeath
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 14:37:51

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New package DepthProc with initial version 1.0
Package: DepthProc
Version: 1.0
Date: 2014-08-18
Title: DepthProc
Author: Daniel Kosiorowski, Mateusz Bocian, Anna Wegrzynkiewicz and Zygmunt Zawadzki from Cracow University of Economics.
Maintainer: Zygmunt Zawadzki
Description: Package for depths
License: GPL-2
Depends: R (>= 3.0.0), ggplot2, Rcpp (>= 0.11.2), rrcov, np, methods, MASS
Imports: lattice, sm, geometry
Suggests: mvtnorm, rgl, sn, robustbase,
LinkingTo: Rcpp, RcppArmadillo
Repository: CRAN
Repository/R-Forge/Project: depthproc
Repository/R-Forge/Revision: 54
Repository/R-Forge/DateTimeStamp: 2014-08-20 09:54:39
Date/Publication: 2014-08-20 14:33:13
Packaged: 2014-08-20 10:15:11 UTC; rforge
NeedsCompilation: yes

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New package rsunlight with initial version 0.3.0
Package: rsunlight
Description: Interface to four Sunlight Foundation APIs (http://sunlightfoundation.com/api/) for government data, including the Congress API v3, the Capitol Words API, the Influence Explorer API, and the Open States API. Sunlight Foundation is a nonpartison nonprofit that collects and provides data on government activities, and those that influence government. Functions are provided to interact with each of the four APIs. rCharts - https://github.com/ramnathv/rCharts
Title: Interface to Sunlight Foundation APIs.
Version: 0.3.0
Date: 2014-08-19
License: MIT + file LICENSE
URL: https://github.com/ropengov/rsunlight
BugReports: https://github.com/ropengov/rsunlight/issues
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"), person("Thomas J.", "Leeper", role=c("ctb"), email="thosjleeper@gmail.com"))
VignetteBuilder: knitr
LazyLoad: yes
LazyData: yes
Imports: httr, plyr, jsonlite, stringr, assertthat
Suggests: knitr, testthat, rCharts
Packaged: 2014-08-20 06:53:38 UTC; sacmac
Author: Scott Chamberlain [aut, cre], Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 10:39:41

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New package RGA with initial version 0.1.1
Package: RGA
Type: Package
Title: A Google Analytics API client for R
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also the RGA package provides shiny app to explore the core reporting API dimensions and metrics.
URL: https://bitbucket.org/unikum/rga
BugReports: https://bitbucket.org/unikum/rga/issues
Version: 0.1.1
Date: 2014-06-03
Authors@R: c( person(given = "Artem", family = "Klevtsov", email = "a.a.klevtsov@gmail.com", role = c("aut", "cre")), person(given = "Philipp", family = "Upravitelev", email = "upravitelev@gmail.com", role = "ctb"), person(given = "Olga", family = "Shramko", email = "ol1709@yahoo.com", role = "ctb"))
License: GPL (>= 2)
Depends: R (>= 2.15.1)
Imports: RCurl, jsonlite, httr (>= 0.3), httpuv, shiny (>= 0.10.0)
Collate: 'auth.R' 'convert.R' 'data.R' 'utils.R' 'url.R' 'query.R' 'get-data.R' 'mgmt.R' 'onload.R' 'package.R' 'report.R' 'shiny.R'
Packaged: 2014-08-20 07:19:17 UTC; xxx
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 10:39:37

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New package matpow with initial version 0.1.1
Package: matpow
Type: Package
Title: matrix powers
Version: 0.1.1
Description: A general framework for computing powers of matrices. A key feature is the capability for users to write callback functions, called after each iteration, thus enabling customization for specific applications. Diverse types of matrix classes/matrix multiplication are accommodated. If the multiplication type computes in parallel, then the package computation is also parallel.
License: GPL (>= 2)
Suggests: bigmemory, gputools
NeedsCompilation: no
ByteCompile: yes
Author: Norm Matloff, Jack Norman
Maintainer: Norm Matloff
Repository: CRAN
Packaged: 2014-08-20 05:53:00 UTC; matloff
Date/Publication: 2014-08-20 08:12:37

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New package x.ent with initial version 0.0.4
Package: x.ent
Type: Package
Title: eXtraction of ENTity
Description: x.ent is a system for extracting information (entities and relations between them) in text datasets. It also emphasizes results exploration with graphical displays. It is a rule-based system and works with hand-made dictionaries and local grammars defined by users. x.ent has been written in perl and use javascript to define user preferences through a browser. Local grammars are defined and compiled with the tool Unitex, developed by University Paris Est, and supporting multiple languages. See ?xconfig for an introduction.
Version: 0.0.4
Date: 2014-07-14
Author: Nicolas Turenne , Tien Phan
Depends: R (>= 3.0.0),opencpu,rJava
Imports: stringr,xtable,jsonlite,venneuler
Maintainer: Tien Phan
License: GPL-3
SystemRequirements: Perl (>= 5.0), Unitex (>= 3.0 http://www-igm.univ-mlv.fr/~unitex/)
Packaged: 2014-08-19 23:26:06 UTC; phantrongtien
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-20 06:12:26

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Tue, 19 Aug 2014

New package DStree with initial version 1.0
Package: DStree
Type: Package
Title: Recursive Partitioning for Discrete-Time Survival Trees
Version: 1.0
Date: 2014-08-19
Author: Peter Mayer, Denis Larocque, Matthias Schmid
Maintainer: Peter Mayer
Description: Building discrete-time survival trees and bagged trees based on the functionalities of the rpart package. Splitting criterion maximizes the likelihood of a covariate-free logistic discrete time hazard model.
License: GPL-2
NeedsCompilation: no
Depends: rpart,pec,Ecdat
Imports: rpart.plot,survival, Rcpp
LazyData: no
LinkingTo: Rcpp
Packaged: 2014-08-19 18:15:30 UTC; Peter
Repository: CRAN
Date/Publication: 2014-08-19 22:25:27

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New package TDA with initial version 1.0
Package: TDA
Type: Package
Title: Statistical Tools for Topological Data Analysis
Version: 1.0
Date: 2014-08-01
Author: Brittany T. Fasy, Fabrizio Lecci
Maintainer: Fabrizio Lecci
Description: This package provides some tools for Topological Data Analysis. In particular it provides functions for the statistical analysis of persistent homology and for density clustering.
Depends: FNN, igraph, parallel, scales
License: GPL (>= 2.0)
Packaged: 2014-08-19 16:16:34 UTC; fabrizio
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-19 19:57:29

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New package RcmdrPlugin.EcoVirtual with initial version 0.1
Package: RcmdrPlugin.EcoVirtual
Type: Package
Title: Rcmdr EcoVirtual Plugin
Version: 0.1
Date: 2014-08-15
Author: Alexandre Adalardo de Oliveira and Paulo Inacio Prado
Maintainer: Alexandre Adalardo de Oliveira
Depends: Rcmdr (>= 1.4-0), EcoVirtual
Description: This package provides an Rcmdr "plug-in" for the EcoVirtual package and was designed primarily for teaching ecological models using simulations.
License: GPL (>= 2)
URL: http://ecovirtual.ib.usp.br
LazyLoad: yes
Packaged: 2014-08-19 11:30:31 UTC; ale
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-19 15:12:37

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New package BAT with initial version 1.0
Package: BAT
Title: Biodiversity Assessment Tools
Version: 1.0
Date: August, 19 2014
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
Description: This package introduces algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or ultrametric trees depicting species relationships.
Depends: R (>= 3.0.0), vegan
License: GPL-3
LazyData: true
Packaged: 2014-08-19 09:16:58 UTC; pcardoso
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-19 13:42:14

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Mon, 18 Aug 2014

New package mvrtn with initial version 1.0
Package: mvrtn
Type: Package
Title: Mean and Variance of Truncated Normal Distribution
Version: 1.0
Date: 2014-08-17
Author: Matthew McLeod
Maintainer: Matthew McLeod
Description: Mean, variance, and random variates for left/right truncated normal distributions.
License: LGPL (>= 2.0, < 3) | Mozilla Public License
Packaged: 2014-08-18 17:35:37 UTC; Matthew
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-18 20:55:28

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New package lmmot with initial version 0.1.1
Package: lmmot
Type: Package
Title: Multiple Ordinal Tobit (MOT) model
Version: 0.1.1
Date: 2014-08-12
Author: Marvin N. Wright
Maintainer: Marvin N. Wright
Description: Fit right censored Multiple Ordinal Tobit (MOT) model.
License: GPL-3
Depends: maxLik, MASS
Packaged: 2014-08-18 14:49:12 UTC; wright
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-18 19:20:37

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New package synthpop with initial version 1.0-0
Package: synthpop
Type: Package
Title: Generating synthetic versions of sensitive microdata for statistical disclosure control
Version: 1.0-0
Date: 2014-08-03
Author: Beata Nowok, Gillian M Raab and Chris Dibben (first two authors in alphabetical order)
Maintainer: Beata Nowok
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data.
License: GPL-2 | GPL-3
Depends: lattice, MASS, methods, nnet
Imports: rpart, party
LazyData: yes
Packaged: 2014-08-18 14:28:06 UTC; bnowok
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-18 17:15:24

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New package LinRegInteractive with initial version 0.1-3
Package: LinRegInteractive
Type: Package
Title: Interactive Interpretation of Linear Regression Models
Version: 0.1-3
Date: 2014-08-18
Author: Martin Meermeyer
Maintainer: Martin Meermeyer
Description: Interactive visualization of effects and marginal effects for linear regression models and of link functions, response functions and marginal effects for generalized linear regression models with binary dependent variables. A major feature is the handling of the effects of categorical covariates: if two or more factors are used as covariates every combination of the levels of each factor is treated separately. The interactive approach, the automatic calculation of marginal effects and far-reaching possibilities to customize the graphical output are characteristic features as well.
License: GPL-2
Depends: R (>= 3.0.0), rpanel (>= 1.1-3)
Suggests: AER
Packaged: 2014-08-18 13:26:26 UTC; meermeyer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-18 16:31:15

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New package wildlifeDI with initial version 0.1
Package: wildlifeDI
Type: Package
Title: Calculate Indices of Dynamic Interaction for Wildlife Telemetry Data
Version: 0.1
Date: 2014-08-15
Author: Jed Long
Maintainer: Jed Long
Description: Dynamic interaction refers to spatial-temporal associations in the movements of two (or more) animals. This package provides tools for calculating a suite of indices used for quantifying dynamic interaction with wildlife telemetry data. For more information on each of the methods employed see the references within. The package draws heavily on the classes and methods developed in the 'adehabitat' packages.
URL: http://www.geog.uvic.ca/spar/dynamicinteraction/
License: GPL-3
VignetteBuilder: knitr
Suggests: knitr, adehabitatHR
Imports: sp, rgeos, adehabitatLT
Packaged: 2014-08-18 09:37:33 UTC; jed long
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-18 13:55:56

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New package rfordummies with initial version 0.0-2
Package: rfordummies
Title: Code examples to accompany the book "R for Dummies"
Version: 0.0-2
Authors@R: c(person("Andrie", "de Vries", role=c("aut", "cre"), email="apdevries@gmail.com"), person("Joris", "Meys", role = c("aut")))
Description: This package contains all the code examples in the book "R for Dummies" (1st edition)
Date: 2014-08-18
URL: http://rfordummies.com
BugReports: https://github.com/andrie/rfordummies/issues
Suggests: fortunes, stringr, sos, XLConnect, reshape2, ggplot2, foreign, lattice
License: GPL-2 | GPL-3
LazyData: true
Packaged: 2014-08-18 09:02:22 UTC; Andrie de Vries
Author: Andrie de Vries [aut, cre], Joris Meys [aut]
Maintainer: Andrie de Vries
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-18 11:11:22

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New package PhyActBedRest with initial version 1.0
Package: PhyActBedRest
Type: Package
Title: Marks periods of sleep in Actigraph accelerometer data
Version: 1.0
Date: 2014-02-11
Author: J. Dustin Tracy, Zhiyi Xu, Leena Choi, Sari Acra, Kong Y. Chen, Maciej S. Buchowski
Maintainer: J. Dustin Tracy
Description: Applies an automated algorithm to mark Actigraph accelerometer data as either bedrest or active. There are separate functions for waist and wrist data. Its input is a dataframe with a timestamp column and one of counts. The output is the same dataframe with an additional column, bedrest. Bedrest will have "a" active or "br" for each line. Options also allow for "n" nap which only differ than "s" in being for a shorter (specifiable) time period. Designed to be used after wearmarking function in Physical Activity package.
License: GPL (>= 3)
Packaged: 2014-08-17 23:55:44 UTC; Dustin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-18 07:26:32

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Sat, 16 Aug 2014

New package RGoogleAnalytics with initial version 0.1.1
Package: RGoogleAnalytics
Version: 0.1.1
Date: 2014-08-16
Title: R Wrapper for the Google Analytics API
Author: Michael Pearmain. Contributions from Nick Mihailowski, Vignesh Prajapati, Kushan Shah and Nicolas Remy
Description: Provides functions for accessing and retrieving data from the Google Analytics API
Maintainer: Kushan Shah
BugReports: https://github.com/Tatvic/RGoogleAnalytics/issues
Depends: R(>= 3.0.2), lubridate, httr
Suggests: testthat
License: Apache License 2.0
NeedsCompilation: no
Repository: CRAN
Packaged: 2014-08-16 14:50:42 UTC; kushan
Date/Publication: 2014-08-16 17:31:12

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New package snpar with initial version 1.0
Package: snpar
Type: Package
Title: Supplementary Non-parametric Statistics Methods
Version: 1.0
Date: 2014-08-11
Author: Debin Qiu
Maintainer: Debin Qiu
Description: contains several supplementary non-parametric statistics methods including quantile test, Cox-Stuart trend test, runs test, normal score test, kernel PDF and CDF estimation, kernel regression estimation and kernel Kolmogorov-Smirnov test.
License: GPL (>= 2)
Packaged: 2014-08-16 08:09:26 UTC; Debin Qiu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-16 10:45:40

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New package RootsExtremaInflections with initial version 1.0
Package: RootsExtremaInflections
Type: Package
Title: Finds roots, extrema and inflection points of a curve
Version: 1.0
Date: 2014-08-16
Author: Demetris T. Christopoulos
Maintainer: Demetris T. Christopoulos
Description: Implementation of the Taylor Regression Estimator method described in Christopoulos (2014,) for finding the root, extreme or inflection point of a curve, when we only have a set of probably noisy xy points for it. The method uses a suitable polynomial regression in order to find the coefficients of the relevant Taylor polynomial for the function that has generated our data.
License: GPL-2
LazyLoad: yes
Packaged: 2014-08-16 06:34:48 UTC; demetris
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-16 09:57:59

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New package RECA with initial version 1.0
Package: RECA
Type: Package
Title: Relevant Component Analysis for Supervised Distance Metric Learning
Version: 1.0
Date: 2014-06-24
Author: Nan Xiao
Maintainer: Nan Xiao
Description: Relevant Component Analysis (RCA) tries to find a linear transformation of the feature space such that the effect of irrelevant variability is reduced in the transformed space.
License: GPL (>= 2)
URL: https://github.com/road2stat/RECA
BugReports: https://github.com/road2stat/RECA/issues
Packaged: 2014-08-16 07:50:56 UTC; jimmy
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-16 10:45:30

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New package EcoVirtual with initial version 0.1
Package: EcoVirtual
Type: Package
Title: Simulation of Ecological Models
Version: 0.1
Date: 2014-08-15
Author: Alexandre Adalardo de Oliveira and Paulo Inacio Prado
Maintainer: Alexandre Adalardo de Oliveira
Description: A package for simulations of classical ecological models as a learning resource.
Depends: tcltk
License: GPL (>= 2)
URL: http//ecovirtual.ib.usp.br
LazyLoad: yes
Packaged: 2014-08-15 21:36:35 UTC; ale
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-16 07:51:36

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Fri, 15 Aug 2014

New package BBEST with initial version 0.1-0
Package: BBEST
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin
Version: 0.1-0
Type: Package
Title: Bayesian Estimation of Incoherent Neutron scattering Backgrounds
Description: In this package we implemented a Bayesian-statistics approach for subtraction of incoherent scattering from neutron total-scattering data. In this approach, the estimated background signal associated with incoherent scattering maximizes the posterior probability, which combines the likelihood of this signal in reciprocal and real spaces with the prior that favors smooth lines.
Date: 2014-08-11
License: GPL-3
Imports: DEoptim, aws, grid, ggplot2, reshape2, shiny, methods
LazyData: yes
Packaged: 2014-08-15 19:15:53 UTC; ang2
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-15 22:38:19

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New package rnrfa with initial version 0.1.0
Package: rnrfa
Type: Package
Title: UK National River Flow Archive data from R
Version: 0.1.0
Date: 2014-04-26
Author: Claudia Vitolo , Matthew Fry
Maintainer: Claudia Vitolo
Description: Utility functions to retrieve data from the UK National River Flow Archive. The package contains R wrappers to the UK NRFA data temporary-API (http://www.ceh.ac.uk/data/nrfa/). There are functions to retrieve stations falling in a bounding box, to generate a map and extracting time series and general information. It also contain the dataset \code{StationSummary}.
Depends: R (>= 3.0.2), utils
Imports: XML2R, RCurl, zoo, rjson, rgdal, sp, stringr
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
URL: http://www.ceh.ac.uk/data/nrfa/
NeedsCompilation: no
Packaged: 2014-08-15 16:31:31 UTC; claudia
Repository: CRAN
Date/Publication: 2014-08-15 20:30:19

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New package pycno with initial version 1.2
Package: pycno
Type: Package
Title: Pycnophylactic Interpolation
Version: 1.2
Date: 2014-08-15
Author: Chris Brunsdon
Maintainer: Chris Brunsdon
Depends: stats, sp, maptools, rgeos
Description: Given a SpatialPolygonsDataFrame and a set of populations for each polygon, compute a population density estimate based on Tobler's pycnophylactic interpolation algorithm. The result is a SpatialGridDataFrame.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-08-15 14:04:40 UTC; chrisbrunsdon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-15 16:30:27

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New package embryogrowth with initial version 5.0
Package: embryogrowth
Type: Package
Title: Tools to analyze the thermal reaction norm of embryo growth
Version: 5.0
Date: 2014-08-15
Author: Marc Girondot
Maintainer: Marc Girondot
Description: Tools to analyze the thermal reaction norm of embryo growth
Depends: deSolve, numDeriv, parallel, phenology, Hmisc, R (>= 2.14.0)
Suggests: coda, optimx, devtools, shiny, entropy
License: GPL-2
LazyData: yes
LazyLoad: yes
Packaged: 2014-08-15 13:54:51 UTC; marc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-15 16:49:36

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New package sld with initial version 0.2.1
Package: sld
Version: 0.2.1
Date: 2014/08/13
Title: Estimation and Use of the Quantile-Based Skew Logistic Distribution
Depends: stats, lmom
Suggests: graphics
Author: Robert King
Maintainer: Robert King
Description: The skew logistic distribution is a quantile-defined generalisation of the logistic distribution (van Staden 2013). Provides random numbers, quantiles, probabilities, densities and density quantiles for the distribution. It provides Quantile-Quantile plots and method of L-Moments estimation for the distribution.
License: GPL (>= 2)
URL: http://tolstoy.newcastle.edu.au/~rking/SLD/
Packaged: 2014-08-13 00:29:35 UTC; robertking
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-15 14:42:03

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New package RcppParallel with initial version 4.2.5.1
Package: RcppParallel
Type: Package
Title: Parallel programming tools for Rcpp
Version: 4.2.5.1
Date: 2014-07-08
Author: JJ Allaire; Romain Francois; Intel, Inc.; Marcus Geelnard
Maintainer: JJ Allaire
Description: High level functions for doing parallel programming with Rcpp. For example, the parallelFor function can be used to convert the work of a standard serial "for" loop into a parallel one and the parallelReduce function can be used for accumulating aggregate or other values.
SystemRequirements: GNU make
License: GPL-2
Collate: 'options.R'
Packaged: 2014-08-15 10:17:31 UTC; jjallaire
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-15 14:41:51

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New package gCat with initial version 0.1
Package: gCat
Version: 0.1
Date: 2014-08-14
Title: Graph-based two-sample tests for categorical data
Author: Hao Chen and Nancy R. Zhang
Maintainer: Hao Chen
Depends: R (>= 3.0.1)
Description: These are two-sample tests for categorical data utilizing similarity information among the categories. They are useful when there is underlying structure on the categories.
License: GPL (>= 2)
Packaged: 2014-08-14 21:43:22 UTC; haochen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-15 07:10:57

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New package CVTuningCov with initial version 1.0
Package: CVTuningCov
Type: Package
Title: Regularized Estimators of Covariance Matrices with CV Tuning
Version: 1.0
Date: 2014-07-31
Author: Binhuan Wang
Maintainer: Binhuan Wang
Description: This is a package for selecting tuning parameters based on cross-validation (CV) in regularized estimators of large covariance matrices. Four regularized methods are implemented: banding, tapering, hard-thresholding and soft-thresholding. Two types of matrix norms are applied: Frobenius norm and operator norm. Two types of CV are considered: K-fold CV and random CV. Usually K-fold CV use K-1 folds to train a model and the rest one fold to validate the model. The reverse version trains a model with 1 fold and validates with the rest with K-1 folds. Random CV randomly splits the data set to two parts, a training set and a validation set with user-specified sizes.
Suggests: MASS
License: GPL-2
Packaged: 2014-08-14 20:23:21 UTC; wangb09
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-15 06:56:38

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Thu, 14 Aug 2014

New package mirtCAT with initial version 0.1
Package: mirtCAT
Version: 0.1
Date: 2014-07-10
Type: Package
Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Authors@R: c( person("Phil", family="Chalmers", email = "rphilip.chalmers@gmail.com", role = c("aut", "cre", "cph")))
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R.
Depends: R (>= 2.15), mirt (>= 1.5), shiny (>= 0.10.0)
Imports: methods
Suggests: testthat
ByteCompile: no
LazyLoad: yes
LazyData: yes
License: GPL (>= 3)
Repository: CRAN
Maintainer: Phil Chalmers
URL: https://github.com/philchalmers/mirtCAT
BugReports: https://github.com/philchalmers/mirtCAT/issues?state=open
Packaged: 2014-08-14 17:43:58 UTC; phil
Author: Phil Chalmers [aut, cre, cph]
NeedsCompilation: no
Date/Publication: 2014-08-14 22:21:49

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New package bamboo with initial version 0.9.5
Package: bamboo
Type: Package
Title: Protein Secondary Structure Prediction Using the Bamboo Method
Version: 0.9.5
Date: 2014-08-14
Author: David B. Dahl
Maintainer: David B. Dahl
URL: http://dahl.byu.edu/software/bamboo/
Imports: rJava, jvmr
SystemRequirements: Java (>= 1.6)
Description: Implementation of the methods described in the paper Li, Dahl, Vannucci, Joo, and Tsai (2014), Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction, PLOS ONE, revise and resubmit.
License: GPL-3
Packaged: 2014-08-14 06:37:44 UTC; dahl
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-14 10:21:35

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New package trimTrees with initial version 1.2
Package: trimTrees
Type: Package
Title: Trimmed opinion pools of trees in a random forest
Version: 1.2
Date: 2014-08-1
Depends: R (>= 2.5.0),stats,randomForest,mlbench
Author: Yael Grushka-Cockayne, Victor Richmond R. Jose, Kenneth C. Lichtendahl Jr. and Huanghui Zeng, based on the source code from the randomForest package by Andy Liaw and Matthew Wiener and on the original Fortran code by Leo Breiman and Adele Cutler.
Maintainer: Yael Grushka-Cockayne
Description: Creates point and probability forecasts from the trees in a random forest using a trimmed opinion pool.
Suggests: MASS
License: GPL (>= 2)
Packaged: 2014-08-13 21:48:25 UTC; lichtendahlc
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-14 07:11:17

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Wed, 13 Aug 2014

New package BlandAltmanLeh with initial version 0.1.0
Package: BlandAltmanLeh
Type: Package
Title: Plots (slightly extended) Bland-Altman plots
Version: 0.1.0
Date: 2014-08-13
Author: Bernhard Lehnert
Maintainer: Bernhard Lehnert
Description: Bland-Altman Plots using base graphics as well as ggplot2, slightly extended by confidence intervals, with detailed return values and a sunflowerplot option for data with ties.
Suggests: ggplot2, knitr
License: GPL
VignetteBuilder: knitr
Packaged: 2014-08-13 15:05:53 UTC; Bernhard
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-13 17:17:31

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New package complmrob with initial version 0.5.4
Package: complmrob
Type: Package
Title: Robust linear regression with compositional data as covariates
Version: 0.5.4
Date: 2014-08-13
Author: David Kepplinger
Maintainer: David Kepplinger
Description: This package provides functionality to perform robust regression on compositional data. To get information on the distribution of the estimates, various bootstrapping methods are implemented for the compositional as well as for standard robust regression models, to provide a direct comparison between them.
License: GPL (>= 2)
Imports: robustbase, ggplot2, boot, parallel, scales
Packaged: 2014-08-13 12:04:26 UTC; david
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-13 14:39:58

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New package tvd with initial version 0.1.0
Package: tvd
Type: Package
Title: Total Variation Denoising
Version: 0.1.0
Date: 2014-08-11
Authors@R: c(person(given = "Mark", family = "Pinese", role = c("aut", "cre", "cph"), email = "m.pinese@garvan.org.au"))
Description: Total Variation Denoising is a regularized denoising method which effectively removes noise from piecewise constant signals whilst preserving edges. This package contains a C++ implementation of Condat's very fast 1D squared error loss TVD algorithm. Additional methods and loss functions may be added in future versions.
License: EPL (>= 1.0)
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp
URL: https://bitbucket.org/marpin/r-tvd
BugReports: https://bitbucket.org/marpin/r-tvd/issues
Packaged: 2014-08-13 09:02:47 UTC; marpin
Author: Mark Pinese [aut, cre, cph]
Maintainer: Mark Pinese
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-13 11:23:42

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New package picasso with initial version 0.1.0
Package: picasso
Type: Package
Title: Pathwise Calibrated Sparse Shooting Algorithm
Version: 0.1.0
Date: 2014-08-12
Author: Xingguo Li, Tuo Zhao and Han Liu
Maintainer: Xingguo Li
Depends: R (>= 2.15.0), lattice, igraph, MASS, Matrix
Description: Implement a new family of efficient algorithms, called PathwIse CalibrAted Sparse Shooting AlgOrithm, for a variety of sparse learning problems, including Sparse Linear Regression, Sparse Logistic Regression, Sparse Column Inverse Operator and Sparse Multivariate Regression. Different types of active set identification schemes are implemented, such as cyclic search, greedy search, stochastic search and proximal gradient search. Besides, the package provides the choices between convex (L1 norm) and non-convex (MCP and SCAD) regularizations. Moreover, group regularization for Sparse Linear Regression and Sparse Logistic Regression are also implemented.
License: GPL-2
Repository: CRAN
Packaged: 2014-08-12 20:36:10 UTC; xingguo
NeedsCompilation: yes
Date/Publication: 2014-08-13 11:05:24

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New package hddtools with initial version 0.1.1
Package: hddtools
Title: Hydrological Data Discovery Tools
Version: 0.1.1
Author: Claudia Vitolo
Maintainer: Claudia Vitolo
Description: Facilitates discovery of hydrological data, non-programmatic access to catalogues and databases.
Depends: R (>= 3.0.2)
Imports: sp, rgdal, raster, RCurl, XML, zoo
License: GPL-3
LazyData: true
Packaged: 2014-08-13 10:41:24 UTC; ripley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-13 12:44:00

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New package edgeRun with initial version 1.0.7
Package: edgeRun
Type: Package
Title: More powerful unconditional testing of negative binomial means for Digital Gene Expression Data
Version: 1.0.7
Date: 2014-08-11
Author: Emmanuel Dimont
Maintainer: Emmanuel Dimont
Description: Extends edgeR functionality by improving on exactTest using an unconditional test of negative binomial means.
License: MIT + file LICENSE
Depends: edgeR, data.table
Packaged: 2014-08-13 08:17:38 UTC; Emmanuel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-13 11:09:55

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Tue, 12 Aug 2014

New package LindenmayeR with initial version 0.1-0
Package: LindenmayeR
Type: Package
Title: Functions to Explore L-Systems (Lindenmayer Systems)
Version: 0.1-0
Date: 2014-08-12
Description: Lindenmayer or L-systems are parallel rewriting systems which can be used to simulate biological forms and certain kinds of fractals. Briefly, in an L-system a series of symbols in a string are replaced iteratively according to rules to give a more complex string. Eventually, the symbols are translated into turtle graphics for plotting. Wikipedia has a very good introduction: en.wikipedia.org/wiki/L-system This package provides basic functions for exploring L-systems.
License: GPL (>= 3)
Depends: stringr, grid
ByteCompile: TRUE
BugReports: https://github.com/bryanhanson/LindenmayeR/issues
Authors@R: c(person("Bryan", "Hanson", role = c("aut", "cre"), email = "hanson@depauw.edu"))
Packaged: 2014-08-12 19:12:00 UTC; bryanhanson
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-12 23:08:07

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New package astrodatR with initial version 0.1
Package: astrodatR
Type: Package
Title: Astronomical Data
Version: 0.1
Date: 2014-08-08
Author: Eric D. Feigelson
Maintainer: "Eric D., Feigelson"
Description: A collection of 19 datasets from contemporary astronomical research. They are described the textbook `Modern Statistical Methods for Astronomy with R Applications' by Eric D. Feigelson and G. Jogesh Babu (Cambridge University Press, 2012, Appendix C) or on the website of Penn State's Center for Astrostatistics (http://astrostatistics.psu.edu/datasets). These datasets can be used to exercise methodology involving: density estimation; heteroscedastic measurement errors; contingency tables; two-sample hypothesis tests; spatial point processes; nonlinear regression; mixture models; censoring and truncation; multivariate analysis; classification and clustering; inhomogeneous Poisson processes; periodic and stochastic time series analysis.
License: GPL
Packaged: 2014-08-12 16:42:12 UTC; e5f
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-12 22:20:23

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New package optmatch with initial version 0.9-3
Package: optmatch
Version: 0.9-3
Date: 2014-08-12
Title: Functions for optimal matching
Author: Ben B. Hansen , Mark Fredrickson , Josh Buckner, Josh Errickson, and Peter Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas and Paul Tseng
Maintainer: Mark M. Fredrickson
Depends: R (>= 2.15.1), stats, methods, graphics, digest
Suggests: boot, RItools, biglm, testthat, survival, brglm, arm
Description: Functions for optimal matching, including full matching
License: file LICENSE
URL: http://www.r-project.org, https://github.com/markmfredrickson/optmatch
Collate: 'abs.optmatch.dlist.R' 'boxplot-methods.R' 'DenseMatrix.R' 'InfinitySparseMatrix.R' 'caliper.R' 'deprecated.R' 'distUnion.R' 'exactMatch.R' 'feasible.R' 'fill.NAs.R' 'fmatch.R' 'fullmatch.R' 'makedist.R' 'matched.distances.R' 'matched.R' 'matchfailed.R' 'match_on.R' 'max.controls.cap.R' 'mdist.R' 'min.controls.cap.R' 'Ops.optmatch.dlist.R' 'Optmatch.R' 'pairmatch.R' 'print.optmatch.dlist.R' 'print.optmatch.R' 'relaxinfo.R' 'scores.R' 'stratumStructure.R' 'subDivStrat.R' 'summary.optmatch.R' 'utilities.R' 'zzzDistanceSpecification.R' 'zzz.R'
Packaged: 2014-08-12 15:35:12 UTC; mark
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-12 18:43:00

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New package swfscMisc with initial version 1.0.1
Package: swfscMisc
Type: Package
Title: Miscellaneous Functions for Southwest Fisheries Science Center
Version: 1.0.1
Date: 2014-08-11
Author: Eric Archer
Maintainer: Eric Archer
Description: Collection of conversion, analytical, geodesic, mapping, and plotting functions. Used to support packages and code written by researchers at the Southwest Fisheries Science Center of the National Oceanic and Atmospheric Administration.
Imports: maps
Depends: mapdata
License: GPL (>= 2)
Packaged: 2014-08-11 21:46:09 UTC; eric.archer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-12 06:53:33

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New package cramer with initial version 0.9-1
Package: cramer
Version: 0.9-1
Date: 2014/08/11
Title: Multivariate nonparametric Cramer-Test for the two-sample-problem
Author: Carsten Franz
Maintainer: Carsten Franz
Depends: R (>= 0.65), boot
Description: Provides R routine for the so called two-sample Cramer-Test. This nonparametric two-sample-test on equality of the underlying distributions can be applied to multivariate data as well as univariate data. It offers two possibilities to approximate the critical value both of which are included in this package.
License: GPL (>= 2)
Packaged: 2014-08-11 21:41:55 UTC; carsten
Repository: CRAN
Date/Publication: 2014-08-12 06:53:32
NeedsCompilation: no

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Mon, 11 Aug 2014

New package vartors with initial version 0.2.6
Package: vartors
Type: Package
Title: Transform Definition of Variables to R Scripts
Version: 0.2.6
Date: 2014-08-10
Authors@R: c(person("Joris", "Muller", email = "joris.muller@etu.unistra.fr", role = c("aut", "cre")), person("Erik-André","Sauleau", role = c("ctb")))
Maintainer: Joris Muller
Description: Generates R scripts useful to perform repetitive tasks on variables of different classes from a simple database. First it helps to create a tabular file describing the variables. Then the package could process this tabulate file to create a script in a .R or .Rmd format. This script will include code blocks for each variable according to the variable description. It could help to import, adapt to R classes and perform descriptive analysis on each variable according to its type. This R script could be used as it is or it could be modified if necessary to perform additional analysis. The user could write his own R script template to produce a customized script.
Depends: R (>= 3.0.2)
Imports: methods
Suggests: testthat, roxygen2, utils, knitr
License: GPL-3
URL: https://github.com/jomuller/vartors
BugReports: https://github.com/jomuller/vartors/issues/new
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
BuildVignettes: true
VignetteBuilder: knitr
Packaged: 2014-08-11 17:25:02 UTC; jomuller
Author: Joris Muller [aut, cre], Erik-André Sauleau [ctb]
Repository: CRAN
Date/Publication: 2014-08-11 21:23:11

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New package LakeMetabolizer with initial version 1.1
Package: LakeMetabolizer
Title: Tools for the analysis of ecosystem metabolism
Maintainer: Luke Winslow
Version: 1.1
Author: Luke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul Hanson, Gordon Holtgrieve, Aline Jaimes, Jordan Read, Richard Woolway
Description: A collection of tools for the calculation of freewater metabolism.
License: GPL (>= 2)
Imports: plyr
Suggests: R2jags
Depends: R (>= 2.15.0), rLakeAnalyzer (>= 1.4)
Packaged: 2014-08-11 15:46:20 UTC; lawinslow
Repository: CRAN
Date/Publication: 2014-08-11 21:38:10
NeedsCompilation: yes

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New package hydrostats with initial version 0.2
Package: hydrostats
Type: Package
Title: Hydrologic indices for daily time series data.
Version: 0.2
Date: 2014-08-14
Author: Nick Bond
Maintainer: Nick Bond
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
License: GPL (>= 2)
Suggests: plyr
Packaged: 2014-08-11 11:35:09 UTC; nickbond
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-11 14:41:09

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New package RcppMLPACK with initial version 1.0.9
Package: RcppMLPACK
Type: Package
Title: Rcpp integration for MLPACK library
Version: 1.0.9
Date: 2014-08-08
Author: Qiang Kou
Maintainer: Qiang Kou
Description: MLPACK is an intuitive, fast, scalable C++ machine learning library, meant to be a machine learning analog to LAPACK. It aims to implement a wide array of machine learning methods and function as a Swiss army knife for machine learning researchers: MLPACK is from http://www.mlpack.org/: sources are included in the package.
License: LGPL (>= 2)
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp, RcppArmadillo, BH
Packaged: 2014-08-10 22:51:10 UTC; qkou
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-11 08:09:12

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New package GrammR with initial version 1.0.0
Package: GrammR
Type: Package
Title: Graphical Representation and Modeling of Metagenomic Reads
Version: 1.0.0
Date: 2014-08-06
Author: Deepak N. Ayyala, Shili Lin, Department of Statistics, The Ohio State University, Columbus, Ohio, USA.
Maintainer: Deepak Nag Ayyala
Description: Represents metagenomic samples on the Euclidean space to examine similarity amongst samples by studying clusters in the model. Given the matrix of metagenomic counts for samples, this package (1) quantifies dissimilarity between samples using Kendall's tau-distance, (2) constructs multidimensional models of different dimension, and (3) plots the models for visualization and comparison.
Depends: R (>= 3.0.0)
Imports: gWidgets, RGtk2, gWidgetsRGtk2, MASS, cluster, rgl, GUniFrac, ape
LazyLoad: YES
License: LGPL-3
Packaged: 2014-08-10 16:28:54 UTC; DeepakNag
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-11 07:49:10

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New package CARBayesST with initial version 1.0
Package: CARBayesST
Type: Package
Title: Poisson Log-linear Models with Spatio-temporal Random Effects
Version: 1.0
Date: 2014-08-05
Author: Duncan Lee
Maintainer: Duncan Lee
Description: Implements a series of Poisson log-linear models with spatio-temporal random effects. The spatial and temporal autocorrelation in the random effects are induced using the class of Conditional AutoRegressive (CAR) priors, which are a special case of Gaussian Markov Random Fields (GMRF). All models are fitted in a Bayesian context using Markov chain Monte Carlo (McMC) simulation.
License: GPL (>= 2)
Depends: R (>= 3.0.0), Rcpp (>= 0.11.2)
Imports: truncdist, coda
LinkingTo: Rcpp
LazyLoad: yes
Packaged: 2014-08-08 12:28:35 UTC; duncan
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-11 08:38:52

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Sun, 10 Aug 2014

New package summarytools with initial version 0.1
Package: summarytools
Type: Package
Title: Dataframe Summaries, Frequency Tables and Numerical Summaries with Customizable Output
Version: 0.1
Date: 2014-08-06
Author: Dominic Comtois
Maintainer: Dominic Comtois
Description: Includes 4 summarizing functions; two are to be used with uni-dimensional data, and the two others with dataframes. For uni-dimensional data, 'unistats' will generate common central tendency statistics and measures of dispersion for numerical data and 'frequencies' will generate a table of frequencies with counts and percentages (including cumulative). Both functions report number and proportion of valid values vs NA values. For dataframes, 'dfSummary' will generate a table containing as many rows as there are columns in the dataframe, each row giving variable information (class and type), labels if any, common statistics for numerical data and frequency tables for any type of data, along with number and proportion of valid (non-missing) values. Finally, 'properties' will conveniently report attributes of a dataframe object itself and also of all its individual components (columns).
Imports: Hmisc, pander, timeDate
License: GPL-2
Packaged: 2014-08-10 19:21:41 UTC; dominic
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-11 00:05:36

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