Wed, 16 Apr 2014

Package VAR.etp updated to version 0.2 with previous version 0.1 dated 2014-04-14

Title: VAR modelling: estimation, testing, and prediction
Description: Estimation, Hypothesis Testing, Prediction for Stationary Vector Autoregressive Models
Author: Jae. H. Kim
Maintainer: Jae H. Kim

Diff between VAR.etp versions 0.1 dated 2014-04-14 and 0.2 dated 2014-04-16

 DESCRIPTION            |    8 ++++----
 MD5                    |   24 +++++++++++++-----------
 R/VAR.LRtest.R         |    6 +++---
 R/VAR.Rest.R           |    2 +-
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 man/VAR.Waldtest.Rd    |    2 +-
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 man/VAR.etp-package.Rd |    4 ++--
 man/dat.Rd             |    2 +-
 14 files changed, 39 insertions(+), 31 deletions(-)

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Package Rcpp11 updated to version 3.1.0.1 with previous version 3.1.0 dated 2014-04-11

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 dated 2014-04-11 and 3.1.0.1 dated 2014-04-16

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Package PopGenome updated to version 2.0.6 with previous version 2.0.5 dated 2014-03-12

Title: A swiss army knife for population genetic & genomic analysis
Description: PopGenome is an R-package for Population Genetic & Genomic Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer

Diff between PopGenome versions 2.0.5 dated 2014-03-12 and 2.0.6 dated 2014-04-16

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 15 files changed, 62 insertions(+), 26 deletions(-)

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Package ModelMap updated to version 3.0.15 with previous version 3.0.14 dated 2014-03-01

Title: Creates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps.
Description: This package will create sophisticated models of training data and validate the models with an independent test set, cross validation, or in the case of Random Forest Models, with Out Of Bag (OOB) predictions on the training data. It will create graphs and tables of the model validation results. It will apply these models to GIS .img files of predictors to create detailed prediction surfaces. It will handle large predictor files for map making, by reading in the .img files in chunks, and output to the .txt file the prediction for each data chunk, before reading the next chunk of data.
Author: Elizabeth Freeman, Tracey Frescino
Maintainer: Elizabeth Freeman

Diff between ModelMap versions 3.0.14 dated 2014-03-01 and 3.0.15 dated 2014-04-16

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 15 files changed, 333 insertions(+), 111 deletions(-)

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Package fanplot updated to version 3.2 with previous version 3.1 dated 2014-03-21

Title: Visualisation of sequential probability distributions using fan charts.
Description: Visualise sequential distributions using a range of plotting styles. Sequential distribution data can be input as either simulations or values corresponding to percentiles over time (columns). Plots are added to existing graphic devices using the fan function. Users can choose from four different styles, including fan chart type plots, where a set of coloured polygon, with shadings corresponding to the percentile values are layered to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel"

Diff between fanplot versions 3.1 dated 2014-03-21 and 3.2 dated 2014-04-16

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More information about fanplot at CRAN
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Package cgam updated to version 1.1 with previous version 1.0 dated 2014-03-05

Title: Constrained Generalized Additive Model
Description: In this package, a constrained generalized additive model is fitted by the cgam routine. Given a set of predictors with or without shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The cone information criterion (CIC) is used to select the best combination of variables and shapes. This package depends on the R package coneproj, in which the hinge algorithm for one cone projection is effected.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao

Diff between cgam versions 1.0 dated 2014-03-05 and 1.1 dated 2014-04-16

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Package scidb updated to version 1.1-2 with previous version 1.1-1 dated 2014-01-25

Title: An R interface to SciDB
Description: SciDB is an open-source array database (http://scidb.org). The scidb package provides an R interface to SciDB.
Author: Paradigm4, B. W. Lewis
Maintainer: B. W. Lewis

Diff between scidb versions 1.1-1 dated 2014-01-25 and 1.1-2 dated 2014-04-16

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Package psd updated to version 0.4-1 with previous version 0.4-0 dated 2013-09-20

Title: Adaptive, sine-multitaper power spectral density estimation
Description: Power spectral density estimates are produced through iterative refinement of the optimal number of sine-tapers at each frequency. The optimization procedure is based on the method of Riedel and Sidorenko (1995), which applies smoothing that varies with frequency to minimize the sum of variance and bias at each point.
Author: Robert L. Parker and Andrew J. Barbour
Maintainer: Andrew J. Barbour

Diff between psd versions 0.4-0 dated 2013-09-20 and 0.4-1 dated 2014-04-16

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Package mizer updated to version 0.2 with previous version 0.1 dated 2013-10-08

Title: Multi-species sIZE spectrum modelling in R
Description: A set of classes and methods to set up and run multispecies, trait based and community size spectrum ecological models, focussed on the marine environment.
Author: Finlay Scott (JRC, IT) and Julia Blanchard (Sheffield University, UK) and Ken Andersen (DTU Aqua, Copenhagen, DK)
Maintainer: Finlay Scott

Diff between mizer versions 0.1 dated 2013-10-08 and 0.2 dated 2014-04-16

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Package AFLPsim updated to version 0.3-3 with previous version 0.2-2 dated 2013-10-29

Title: Hybrid simulation and genome scan for dominant markers
Description: This package is developed in the Plant Reproductive Biology Lab (RNM-214) - University of Seville. It contains hybrid simulation functions for dominant genetic data. It also provides several genome scan methods.
Author: Francisco Balao [aut, cre], Juan Luis García-Castaño [aut]
Maintainer: Francisco Balao

Diff between AFLPsim versions 0.2-2 dated 2013-10-29 and 0.3-3 dated 2014-04-16

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New package BEQI2 with initial version 1.0-0
Package: BEQI2
Type: Package
Title: Benthic Ecosystem Quality Index 2
Description: Benthic Ecosystem Quality Index 2. This package facilitates the analysis of benthos data. It estimates several quality indices like the total abundance of species, species richness, Shannon index, AZTI Marine Biotic Index (AMBI), and the BEQI-2 index. The package includes two additional optional features that enhance data preprocessing: (1) genus to species conversion, i.e.,taxa counts at the taxonomic genus level can optionally be converted to the species level and (2) pooling: small samples are combined to bigger samples with a standardized size to (a) meet the data requirements of the AMBI, (b) generate comparable species richness values and (c) give a higher benthos signal to noise ratio.
Version: 1.0-0
Date: 2014-04-16
Authors@R: c(person(given = "Willem", family = "van Loon", email = "willem.van.loon@rws.nl", role = c("aut", "cph")), person(given = "Dennis", family = "Walvoort", email = "dennis.Walvoort@wur.nl", role = c("aut", "cre")))
Depends: R (>= 3.0.2), methods, tcltk
Imports: knitr, markdown, RJSONIO, xtable, plyr, reshape2
Suggests: testthat
VignetteBuilder: knitr
License: GPL (>= 3)
Packaged: 2014-04-16 14:38:31 UTC; dennis
Author: Willem van Loon [aut, cph], Dennis Walvoort [aut, cre]
Maintainer: Dennis Walvoort
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-16 22:50:45

More information about BEQI2 at CRAN
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Package greport updated to version 0.5-1 with previous version 0.5-0 dated 2014-03-02

Title: Graphical Reporting for Clinical Trials
Description: The greport package contains many functions useful for monitoring and reporting the results of clinical trials and other experiments in which treatments are compared. LaTeX is used to typeset the resulting reports, recommended to be in the context of knitr. The Hmisc and lattice packages are used by greport for high-level graphics.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr

Diff between greport versions 0.5-0 dated 2014-03-02 and 0.5-1 dated 2014-04-16

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 R/nriskReport.r         |only
 R/survReport.r          |   40 ++---------
 README.md               |   21 +++++
 inst/feh.bib            |only
 man/Merge.Rd            |   48 ++++++++-----
 man/accrualReport.Rd    |   11 ++-
 man/exReport.Rd         |   24 +++++-
 man/greport.Rd          |only
 man/nriskReport.Rd      |only
 man/setgreportOption.Rd |    6 +
 man/startPlot.Rd        |    2 
 man/survReport.Rd       |    4 -
 tests/report.Rnw        |   26 +++----
 tests/test.Rnw          |   35 +++++----
 25 files changed, 399 insertions(+), 223 deletions(-)

More information about greport at CRAN
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Package Rdpack updated to version 0.4-14 with previous version 0.4-4 dated 2013-04-13

Title: Update and manipulate Rd documentation objects
Description: Functions for manipulation of Rd objects, including function reprompt for updating existing Rd documentation for functions, methods and classes, and function rebib for import of references from Bibtex files.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov

Diff between Rdpack versions 0.4-4 dated 2013-04-13 and 0.4-14 dated 2014-04-16

 Rdpack-0.4-14/Rdpack/DESCRIPTION                         |   19 +-
 Rdpack-0.4-14/Rdpack/MD5                                 |   84 ++++++-----
 Rdpack-0.4-14/Rdpack/NAMESPACE                           |  110 ++++++++++++++-
 Rdpack-0.4-14/Rdpack/NEWS                                |   33 ++++
 Rdpack-0.4-14/Rdpack/R/Rdo2Rdf.R                         |    9 -
 Rdpack-0.4-14/Rdpack/R/alias.R                           |    2 
 Rdpack-0.4-14/Rdpack/R/bib.R                             |   11 -
 Rdpack-0.4-14/Rdpack/R/inspect.R                         |   10 -
 Rdpack-0.4-14/Rdpack/R/manip.R                           |   45 ++++--
 Rdpack-0.4-14/Rdpack/R/parse.R                           |    2 
 Rdpack-0.4-14/Rdpack/R/repromptAny.R                     |    5 
 Rdpack-0.4-14/Rdpack/R/sections.R                        |    6 
 Rdpack-0.4-14/Rdpack/R/threedots.R                       |only
 Rdpack-0.4-14/Rdpack/R/usage.R                           |   10 +
 Rdpack-0.4-14/Rdpack/R/utils.R                           |    9 -
 Rdpack-0.4-14/Rdpack/R/yytransient.R                     |only
 Rdpack-0.4-14/Rdpack/R/zzobsolete.R                      |   71 +++++++++
 Rdpack-0.4-14/Rdpack/build/partial.rdb                   |binary
 Rdpack-0.4-14/Rdpack/man/Rd_combo.Rd                     |   10 -
 Rdpack-0.4-14/Rdpack/man/Rdo_collect_metadata.Rd         |only
 Rdpack-0.4-14/Rdpack/man/Rdo_empty_sections.Rd           |    2 
 Rdpack-0.4-14/Rdpack/man/Rdo_get_argument_names.Rd       |only
 Rdpack-0.4-14/Rdpack/man/Rdo_get_item_labels.Rd          |only
 Rdpack-0.4-14/Rdpack/man/Rdo_locate.Rd                   |   48 ++++--
 Rdpack-0.4-14/Rdpack/man/Rdo_locate_leaves.Rd            |    9 -
 Rdpack-0.4-14/Rdpack/man/Rdo_sections.Rd                 |   47 +++++-
 Rdpack-0.4-14/Rdpack/man/Rdo_tags.Rd                     |only
 Rdpack-0.4-14/Rdpack/man/Rdo_which.Rd                    |only
 Rdpack-0.4-14/Rdpack/man/Rdpack-package.Rd               |   66 ++++-----
 Rdpack-0.4-14/Rdpack/man/Rdreplace_section.Rd            |only
 Rdpack-0.4-14/Rdpack/man/c_Rd.Rd                         |   20 +-
 Rdpack-0.4-14/Rdpack/man/compare_usage1.Rd               |    4 
 Rdpack-0.4-14/Rdpack/man/deparse_usage.Rd                |    2 
 Rdpack-0.4-14/Rdpack/man/format_funusage.Rd              |    2 
 Rdpack-0.4-14/Rdpack/man/get_sig_text.Rd                 |    2 
 Rdpack-0.4-14/Rdpack/man/get_usage_text.Rd               |    2 
 Rdpack-0.4-14/Rdpack/man/inspect_args.Rd                 |    2 
 Rdpack-0.4-14/Rdpack/man/inspect_signatures.Rd           |    3 
 Rdpack-0.4-14/Rdpack/man/inspect_slots.Rd                |    3 
 Rdpack-0.4-14/Rdpack/man/inspect_usage.Rd                |    2 
 Rdpack-0.4-14/Rdpack/man/parse_usage_text.Rd             |    2 
 Rdpack-0.4-14/Rdpack/man/predefined.Rd                   |   38 ++++-
 Rdpack-0.4-14/Rdpack/man/promptPackageSexpr.Rd           |    1 
 Rdpack-0.4-14/Rdpack/man/rebib.Rd                        |   19 +-
 Rdpack-0.4-14/Rdpack/man/reprompt.Rd                     |    1 
 Rdpack-0.4-14/Rdpack/man/update_aliases_tmp.Rd           |    2 
 Rdpack-0.4-4/Rdpack/man/Rdo_collect_aliases.Rd           |only
 Rdpack-0.4-4/Rdpack/man/Rdo_locate_predefined_section.Rd |only
 48 files changed, 526 insertions(+), 187 deletions(-)

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New package RHive with initial version 2.0-0.0
Package: RHive
Type: Package
Title: R and Hive
Version: 2.0-0.0
Description: RHive is an R extension facilitating distributed computing via HIVE query. It provides an easy to use HQL like SQL and R objects and functions in HQL.
Author: NexR
Maintainer: Johan Ahn
License: Apache License (== 2.0)
Depends: R (>= 2.13.0), rJava (>= 0.9-0)
Suggests: RUnit
SystemRequirements: Hadoop core >= 0.20.3 (http://hadoop.apache.org/core/), Hive >= 0.8 (http://hive.apache.org/)
OS_type: unix
Repository: CRAN
Packaged: 2014-04-15 01:26:27 UTC; root
NeedsCompilation: no
X-CRAN-Comment: Archived 2013-08-07 as the former maintainer withdrew maintaienrship and the nominated new maintainer did never respond to requests to update the package.
Date/Publication: 2014-04-16 09:21:53

More information about RHive at CRAN
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New package bigalgebra with initial version 0.8.4
Package: bigalgebra
Version: 0.8.4
Date: 2014-04-15
Title: BLAS routines for native R matrices and big.matrix objects.
Author: Michael J. Kane, Bryan Lewis, and John W. Emerson
Maintainer: Michael J. Kane
Imports: methods
Depends: bigmemory (>= 4.0.0)
LinkingTo: bigmemory, BH
Description: This package provides arithmetic functions for R matrix and big.matrix objects.
License: LGPL-3 | Apache License 2.0
Copyright: (C) 2014 Michael J. Kane, Bryan Lewis, and John W. Emerson
URL: http://www.bigmemory.org
LazyLoad: yes
Packaged: 2012-12-26 22:17:06 UTC; blewis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-16 09:21:50

More information about bigalgebra at CRAN
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