Tue, 22 Jul 2014

Package sweSCB updated to version 0.3.5 with previous version 0.3.4 dated 2014-04-15

Title: An R interface to the web API of Statistics Sweden
Description: Interface for the REST API of Statistics Sweden. The package offers methods to fetch information about the data hierarchy stored behind the API; extract metadata; fetch actual data; and clean up the results.
Author: Love Hansson, Thomas Reinholdsson, Mans Magnusson
Maintainer: Mans Magnusson

Diff between sweSCB versions 0.3.4 dated 2014-04-15 and 0.3.5 dated 2014-07-22

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
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 README.md   |   10 +++++-----
 4 files changed, 14 insertions(+), 14 deletions(-)

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Package spartan updated to version 2.0 with previous version 1.3 dated 2014-03-19

Title: Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk.Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden

Diff between spartan versions 1.3 dated 2014-03-19 and 2.0 dated 2014-07-22

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Package SIS updated to version 0.7-3 with previous version 0.7-2 dated 2014-05-06

Title: Sure Independence Screening
Description: (Iterative) Sure Independence Screening for Generalized Linear Models and Cox's Proportional Hazards Models
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana

Diff between SIS versions 0.7-2 dated 2014-05-06 and 0.7-3 dated 2014-07-22

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Package deltaPlotR updated to version 1.4 with previous version 1.3 dated 2013-07-22

Title: Identification of dichotomous differential item functioning (DIF) using Angoff's Delta Plot method
Description: The deltaPlotR package proposes an implementation of Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported.
Author: David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France)
Maintainer: David Magis

Diff between deltaPlotR versions 1.3 dated 2013-07-22 and 1.4 dated 2014-07-22

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 man/adjustExtreme.Rd      |    4 ++++
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New package jSonarR with initial version 1.0
Package: jSonarR
Type: Package
Title: jSonar Analytics Platform API for R
Version: 1.0
Date: 2014-07-02
Author: jSonar Inc.
Maintainer: Dylan McCall
Description: This package enables users to access MongoDB by running queries and returning their results in R data frames. Usually, data in MongoDB is only available in the form of a JSON document. jSonarR uses data processing and conversion capabilities in the jSonar Analytics Platform and the JSON Studio Gateway (http://www.jsonstudio.com), to convert it to a tabular format which is easy to use with existing R packages.
Depends: R (>= 2.12.1), RCurl, methods
SystemRequirements: MongoDB, JSON Studio
Copyright: jSonar Inc.
License: AGPL-3
URL: http://www.jsonstudio.com/
Packaged: 2014-07-22 21:26:38 UTC; dylan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-23 00:40:43

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Package SPACECAP updated to version 1.1.0 with previous version 1.0.6 dated 2012-06-14

Title: A Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models
Description: SPACECAP is a user-friendly software package for estimating animal densities using closed model capture-recapture sampling based on photographic captures using Bayesian spatially-explicit capture-recapture models. This approach offers advantage such as: substantially dealing with problems posed by individual heterogeneity in capture probabilities in conventional capture-recapture analyses. It also offers non-asymptotic inferences which are more appropriate for small samples of capture data typical of photo-capture studies.
Author: Arjun M. Gopalaswamy, Andrew J. Royle, Michael E. Meredith, Pallavi Singh, Devcharan Jathanna, N. Samba Kumar and K. Ullas Karanth
Maintainer: Arjun M. Gopalaswamy

Diff between SPACECAP versions 1.0.6 dated 2012-06-14 and 1.1.0 dated 2014-07-22

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New package RMRAINGEN with initial version 1.0
Package: RMRAINGEN
Maintainer: Emanuele Cordano
License: GPL (>= 2)
Title: RMRAINGEN (R Multi-site RAINfall GENeretor): a package to generate daily time series of rainfall from monthly mean values
Type: Package
Author: Emanuele Cordano
Description: This package contains functions and S3 methods for spatial multi-site stochastic generation of daily precipitation. It generates precipitation occurrence in several sites using Wilks' Approach (1998). Bugs/comments/questions/collaboration of any kind are warmly welcomed.
Version: 1.0
Repository: CRAN
Date: 2014-07-22
Depends: R (>= 3.0), copula, RGENERATE,RMAWGEN,blockmatrix,Matrix
URL: https://github.com/ecor/RMRAINGEN
Packaged: 2014-07-22 14:35:22 UTC; ecor
NeedsCompilation: no
Date/Publication: 2014-07-22 21:18:30

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Package Rcpp11 updated to version 3.1.1 with previous version 3.1.0.1 dated 2014-04-16

Title: R and C++11
Description: Rcpp11 includes a header only C++11 library that facilitates integration between R and modern C++.
Author: Romain Francois [aut, cre], Kevin Ushey [aut], John Chambers [ctb]
Maintainer: Romain Francois

Diff between Rcpp11 versions 3.1.0.1 dated 2014-04-16 and 3.1.1 dated 2014-07-22

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 Rcpp11-3.1.1/Rcpp11/DESCRIPTION                                                              |   10 
 Rcpp11-3.1.1/Rcpp11/MD5                                                                      |  443 ++++------
 Rcpp11-3.1.1/Rcpp11/README.md                                                                |    4 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/ifelse.h                               |  394 --------
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/import.h                               |  105 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/is.h                                   |only
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/lapply.h                               |   38 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/mapply.h                               |  289 ++++++
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/match.h                                |   36 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/materialize.h                          |only
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/mean.h                                 |  131 ++
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/min.h                                  |   79 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/na_omit.h                              |   59 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/parallel.h                             |only
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/pmax.h                                 |  206 ----
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/pow.h                                  |   76 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/range.h                                |   94 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/rep_each.h                             |   99 +-
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/rep_len.h                              |  147 ++-
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/replicate.h                            |   76 +
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/rev.h                                  |   40 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sapply.h                               |  267 +++---
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/seq_along.h                            |   64 +
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/setdiff.h                              |  247 ++---
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sign.h                                 |   63 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sum.h                                  |  152 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/table.h                                |  102 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/tail.h                                 |   46 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/transform.h                            |  112 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/unique.h                               |   30 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/var.h                                  |   34 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/which_max.h                            |   99 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/which_min.h                            |   99 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/col.h                                     |   14 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/diag.h                                    |   65 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/lower_tri.h                               |   21 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/outer.h                                   |   37 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/row.h                                     |   14 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/upper_tri.h                               |   18 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/nona/nona.h                                      |   90 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/operators/logical_operators__Vector__Vector.h    |  152 ---
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h |  321 +------
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/operators/operators.h                            |   15 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/operators/unary_Vector.h                         |only
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/sugar.h                                          |    6 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/undoRmath.h                                      |    3 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/get_na.h                                        |   52 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/index_sequence_that.h                           |only
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/is_finite.h                                     |    2 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/is_na.h                                         |    2 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/is_primitive.h                                  |   20 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/is_vector_expression.h                          |    4 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/mapply_scalar_type.h                            |only
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/number_to_type.h                                |    2 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/r_sexptype_traits.h                             |    6 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/traits/r_type_traits.h                                 |   54 -
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/MatrixRow.h                                     |   35 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/StrideIterator.h                                |   18 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/SugarMatrixExpression.h                         |   16 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/SugarVectorExpression.h                         |   21 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/CharacterVector.h                          |  118 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/ExpressionVector.h                         |  118 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/List.h                                     |  113 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/LogicalVector.h                            |only
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/SimpleVector.h                             |  137 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/is_materialized.h                               |    8 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/make_subsetter_proxy.h                          |only
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/string_proxy.h                                  |  176 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/ContainerWrapper.h                                |    5 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/EnumWrapper.h                                     |    4 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/MatrixWrapper.h                                   |   68 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/PrimitiveWrapper.h                                |    5 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/SexpConvertibleWrapper.h                          |    2 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/Wrapper.h                                         |    3 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/forward.h                                         |   11 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/make_charsexp.h                                   |   14 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/wrap.h                                            |    5 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/wrap_impl.h                                       |   13 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp11                                                      |only
 262 files changed, 4387 insertions(+), 5963 deletions(-)

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New package nontargetData with initial version 1.1
Package: nontargetData
Type: Package
Title: Quantized simulation data of isotope pattern centroids
Version: 1.1
Date: 2014-07-22
Author: Martin Loos, Francesco Corona
Maintainer: Martin Loos
Description: Data sets for isotope pattern grouping of LC-HRMS peaks with package nontarget. Based on a vast set of unique PubChem molecular formulas, quantized (a) m/z, (b) m/z differences, (c) intensity ratios and (d) marker centroids of simulated centroid pairs are listed for different instrument resolutions.
License: GPL-3
Packaged: 2014-07-22 13:59:18 UTC; uchemadmin
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 21:18:38

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Package kinship2 updated to version 1.6.0 with previous version 1.5.7 dated 2014-03-20

Title: Pedigree functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell

Diff between kinship2 versions 1.5.7 dated 2014-03-20 and 1.6.0 dated 2014-07-22

 DESCRIPTION        |    8 ++++----
 MD5                |   22 ++++++++++++----------
 NAMESPACE          |    3 ++-
 R/align.pedigree.R |    8 ++++++--
 R/ped2df.R         |    3 ---
 R/pedigree.R       |    1 +
 inst/NEWS.Rd       |   13 +++++++++++++
 man/familycheck.Rd |   51 ++++++++++++++++++---------------------------------
 noweb/align.Rnw    |    8 ++++++--
 noweb/all.nw       |   23 +++++++++++++++++------
 noweb/pedigree.Rnw |   15 +++++++++++----
 tests/ped1.pdf     |only
 tests/ped2.pdf     |only
 13 files changed, 90 insertions(+), 65 deletions(-)

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New package MixGHD with initial version 1.0
Package: MixGHD
Type: Package
Title: Model based clustering and classification using the mixture of generalized hyperbolic distributions.
Version: 1.0
Date: 2014-07-15
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora
Description: Carries out model-based clustering using three different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Depends: Bessel, stats, MASS, mvtnorm, ghyp, numDeriv, R (>= 3.1.1)
NeedsCompilation: no
License: GPL (>= 2)
Packaged: 2014-07-22 13:24:40 UTC; cristina
Repository: CRAN
Date/Publication: 2014-07-22 21:18:29

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Package heatmapFit updated to version 2.0 with previous version 1.0 dated 2012-11-20

Title: Fit statistic for binary dependent variable models
Description: Generates a fit plot for diagnosing misspecification in models of binary dependent variables, and calculates the related heatmap fit statistic (Esarey and Pierce, 2012).
Author: Justin Esarey [aut, cre], Andrew Pierce [aut], Jericho Du [aut]
Maintainer: Justin Esarey

Diff between heatmapFit versions 1.0 dated 2012-11-20 and 2.0 dated 2014-07-22

 heatmapFit-1.0/heatmapFit/R/Package.R             |only
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 heatmapFit-2.0/heatmapFit/MD5                     |   13 +++++---
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 12 files changed, 28 insertions(+), 22 deletions(-)

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New package FreeSortR with initial version 1.0
Package: FreeSortR
Type: Package
Title: Free Sorting data analysis.
Version: 1.0
Date: 2014-04-29
Author: Philippe Courcoux
Maintainer: Philippe Courcoux
Description: The package FreeSortR provides tools for describing and analysing free sorting data. Main methods are computation of consensus partition and factorial analysis of the dissimilarity matrix between stimuli (using multidimensional scaling approach).
License: GPL-2
Depends: methods, smacof, vegan, ellipse
Packaged: 2014-07-22 14:33:58 UTC; courcoux
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 21:18:25

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Package clinfun updated to version 1.0.6 with previous version 1.0.5 dated 2013-04-16

Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan

Diff between clinfun versions 1.0.5 dated 2013-04-16 and 1.0.6 dated 2014-07-22

 CHANGES                  |    6 ++++++
 DESCRIPTION              |    9 ++++-----
 MD5                      |    8 ++++----
 R/jonkheere.R            |    6 +++---
 man/gsdesign-internal.Rd |   13 ++++++++-----
 5 files changed, 25 insertions(+), 17 deletions(-)

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New package rnbn with initial version 1.0.0
Package: rnbn
Type: Package
Title: Access NBN data
Version: 1.0.0
Date: 2014-07-22
Author: Stuart Ball & Tom August
Maintainer: Tom August
Description: Access to data held by the National Biodiversity Network (NBN, www.nbn.org.uk). The NBN acts as a data warehouse for biological records data in the UK and is the UK node of GBIF (Global Biodiversity Information Facility). In this package NBN data is accessed via its web-services.
License: MIT + file LICENSE
Depends: RCurl, RJSONIO, tcltk
BuildVignettes: FALSE
LazyData: TRUE
Packaged: 2014-07-22 12:02:46 UTC; tomaug
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 14:29:38

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Package llama updated to version 0.7 with previous version 0.6 dated 2014-04-29

Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre], Bernd Bischl [aut], Barry Hurley [ctb], Talal Rahwan [ctb]
Maintainer: Lars Kotthoff

Diff between llama versions 0.6 dated 2014-04-29 and 0.7 dated 2014-07-22

 llama-0.6/llama/inst/tests                        |only
 llama-0.7/llama/DESCRIPTION                       |   17 ++---
 llama-0.7/llama/MD5                               |   73 +++++++++++-----------
 llama-0.7/llama/NAMESPACE                         |    2 
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 llama-0.7/llama/R/classify.R                      |   70 ++++++++++++++-------
 llama-0.7/llama/R/classifyPairs.R                 |   72 ++++++++++++++-------
 llama-0.7/llama/R/cluster.R                       |   48 +++++++-------
 llama-0.7/llama/R/imputeCensored.R                |   12 ++-
 llama-0.7/llama/R/regression.R                    |   54 ++++++++++------
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 llama-0.7/llama/man/classify.Rd                   |   35 ++++++----
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 llama-0.7/llama/man/cluster.Rd                    |   44 ++++++-------
 llama-0.7/llama/man/imputeCensored.Rd             |    8 --
 llama-0.7/llama/man/llama-package.Rd              |   38 +++--------
 llama-0.7/llama/man/misclassificationPenalties.Rd |    8 --
 llama-0.7/llama/man/normalize.Rd                  |    6 -
 llama-0.7/llama/man/parscores.Rd                  |   12 +--
 llama-0.7/llama/man/regression.Rd                 |   42 ++++++------
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 llama-0.7/llama/man/successes.Rd                  |    8 --
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 25 files changed, 322 insertions(+), 259 deletions(-)

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Package Bergm updated to version 2.9 with previous version 2.8 dated 2014-07-02

Title: Bayesian analysis for exponential random graph models
Description: Set of tools to analyse Bayesian exponential random graph models
Author: Alberto Caimo and Nial Friel
Maintainer: Alberto Caimo

Diff between Bergm versions 2.8 dated 2014-07-02 and 2.9 dated 2014-07-22

 DESCRIPTION          |   10 +++++-----
 MD5                  |   23 ++++++++++++++---------
 R/abergm.R           |   22 ++++++++--------------
 R/bbeta.R            |only
 R/bbeta.output.R     |only
 R/bergm.R            |    2 +-
 R/bergm.output.R     |    8 +++++++-
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 man/bergmS.Rd        |   11 +++++------
 15 files changed, 61 insertions(+), 55 deletions(-)

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Package AdaptFitOS updated to version 0.54 with previous version 0.50 dated 2014-03-19

Title: Adaptive Semiparametric Regression with Simultaneous Confidence Bands
Description: Based on the function "asp" of the AdaptFit package fits semiparametric regression models with spatially adaptive penalized splines and computes simultaneous confidence bands.
Author: Manuel Wiesenfarth and Tatyana Krivobokova
Maintainer: Manuel Wiesenfarth

Diff between AdaptFitOS versions 0.50 dated 2014-03-19 and 0.54 dated 2014-07-22

 DESCRIPTION               |   10 
 MD5                       |   62 ++--
 R/almeAux.R               |  126 ++++-----
 R/arg.searchOS.r          |  117 ++++----
 R/asp-internal.r          |    6 
 R/asp2.r                  |    2 
 R/aspHetero.r             |   25 -
 R/aspOS.r                 |    4 
 R/aspmFormReadOS.r        |    5 
 R/firstlib.r              |    2 
 R/fitted.asp.r            |   14 -
 R/plot.scbTest.r          |    4 
 R/plot.scbm.r             |    3 
 R/predict.asp.r           |  591 ++++++++++++++++++++++---------------------
 R/print.asp.r             |   55 +---
 R/residuals.asp.r         |   32 --
 R/scbM.r                  |   15 -
 R/scbTest.r               |   17 -
 R/spmArgReadOS.r          |   47 +--
 R/spmDesignOS.r           |  625 ++++++++++++++++++++++------------------------
 R/spmOS.r                 |    5 
 R/summary.asp.r           |  582 +++++++++++++++++++++---------------------
 man/AdaptFitOS-package.Rd |   32 +-
 man/asp2.Rd               |   39 +-
 man/aspHetero.Rd          |   11 
 man/fitted.asp.Rd         |   15 -
 man/plot.asp.Rd           |   21 -
 man/predict.asp.Rd        |    5 
 man/residuals.asp.Rd      |   16 -
 man/scbM.Rd               |   24 +
 man/sigma.Rd              |    2 
 man/summary.asp.Rd        |    7 
 32 files changed, 1216 insertions(+), 1305 deletions(-)

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Package rplos updated to version 0.4.1 with previous version 0.4.0 dated 2014-05-13

Title: Interface to PLoS Journals search API.
Description: A programmatic interface to the Web Service methods provided by the Public Library of Science journals for search.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain

Diff between rplos versions 0.4.0 dated 2014-05-13 and 0.4.1 dated 2014-07-22

 rplos-0.4.0/rplos/tests/test-all.R                   |only
 rplos-0.4.1/rplos/DESCRIPTION                        |    9 +-
 rplos-0.4.1/rplos/MD5                                |   66 +++++++++----------
 rplos-0.4.1/rplos/NAMESPACE                          |    2 
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New package nycflights13 with initial version 0.1
Package: nycflights13
Title: Data about flights departing NYC in 2013.
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: Airline on-time data for all flights departing NYC in 2013. Also includes useful metadata on airlines, airports, weather, and planes.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
Suggests: dplyr
URL: http://github.com/hadley/nycflights13
Packaged: 2014-07-21 19:26:17 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:54

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New package nasaweather with initial version 0.1
Package: nasaweather
Title: Collection of datasets from the ASA 2006 data expo
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: This package contains tidied data from the ASA 2006 data expo, as well as a number of useful other related data sets.
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
URL: http://github.com/hadley/nasaweather, http://stat-computing.org/dataexpo/2006/
Packaged: 2014-07-21 19:30:24 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:36

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Package mewAvg updated to version 0.3.0 with previous version 0.2.0 dated 2014-01-24

Title: A Fixed Memeory Moving Expanding Window Average
Description: Computes the average of a sequence of random vectors in a moving expanding window using a fixed amount of storage
Author: Adam L. Pintar and Zachary H. Levine
Maintainer: Adam L. Pintar

Diff between mewAvg versions 0.2.0 dated 2014-01-24 and 0.3.0 dated 2014-07-22

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Package leapp updated to version 1.2 with previous version 1.1 dated 2014-01-06

Title: latent effect adjustment after primary projection
Description: These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
Author: Yunting Sun , Nancy R.Zhang , Art B.Owen
Maintainer: Yunting Sun

Diff between leapp versions 1.1 dated 2014-01-06 and 1.2 dated 2014-07-22

 DESCRIPTION |   10 +++++-----
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 4 files changed, 15 insertions(+), 11 deletions(-)

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Package jsonlite updated to version 0.9.9 with previous version 0.9.8 dated 2014-06-02

Title: A smarter JSON encoder/decoder for R
Description: This package is a fork of the RJSONIO package by Duncan Temple Lang. It builds on the same libjson c++ parser, but implements a smarter mapping between JSON data and R classes. The vignette describes the behavior in great detail. In addition to drop-in replacements for toJSON and fromJSON, the package contains funtions to validate, prettify and minify JSON, and many unit tests to verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Jonathan Wallace
Maintainer: Jeroen Ooms

Diff between jsonlite versions 0.9.8 dated 2014-06-02 and 0.9.9 dated 2014-07-22

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Package glasso updated to version 1.8 with previous version 1.7 dated 2011-09-14

Title: Graphical lasso- estimation of Gaussian graphical models
Description: Graphical lasso
Author: Jerome Friedman, Trevor Hastie and Rob Tibshirani
Maintainer: Rob Tibshirani

Diff between glasso versions 1.7 dated 2011-09-14 and 1.8 dated 2014-07-22

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 12 files changed, 2205 insertions(+), 1418 deletions(-)

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New package fueleconomy with initial version 0.1
Package: fueleconomy
Title: EPA fuel economy data
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: Fuel economy data from the EPA, 1985-2015, conveniently packaged for consumption by R users.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
Suggests: dplyr
URL: http://github.com/hadley/fueleconomy
Packaged: 2014-07-21 19:31:13 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:43

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Package COUNT updated to version 1.3.1 with previous version 1.3.0 dated 2014-07-16

Title: Functions, data and code for count data.
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2-nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe
Maintainer: Andrew Robinson

Diff between COUNT versions 1.3.0 dated 2014-07-16 and 1.3.1 dated 2014-07-22

 DESCRIPTION                          |   12 ++++++------
 MD5                                  |    3 ++-
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 3 files changed, 8 insertions(+), 7 deletions(-)

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New package babynames with initial version 0.1
Package: babynames
Title: US baby names 1880-2013
Version: 0.1
Authors@R: 'Hadley Wickham [aut,cre]'
Description: US baby names provided by the SSA. This package contains all names used for at least 5 children of either sex.
Depends: R (>= 3.1.0)
License: CC0
LazyData: true
URL: http://github.com/hadley/babynames
Packaged: 2014-07-21 19:46:18 UTC; hadley
Author: 'Hadley Wickham' [aut, cre]
Maintainer: 'Hadley Wickham'
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-22 11:08:48

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