Mon, 29 Dec 2014

Package TBSSurvival updated to version 1.2 with previous version 1.1 dated 2013-04-17

Title: Survival Analysis using a Transform-Both-Sides model
Description: Functions to perform the reliability/survival analysis using a parametric Transform-both-sides (TBS) model.
Author: Adriano Polpo , Cassio de Campos , D. Sinha , Stuart Lipsitz , Jianchang Lin
Maintainer: Cassio de Campos

Diff between TBSSurvival versions 1.1 dated 2013-04-17 and 1.2 dated 2014-12-29

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New package metabolomics with initial version 0.1.4
Package: metabolomics
Type: Package
Title: Analysis of Metabolomics Data
Version: 0.1.4
Date: 2014-12-27
Author: Alysha M De Livera and Jairus B Bowne
Maintainer: Alysha M De Livera
Description: A collection of functions to aid in the statistical analysis of metabolomic data
License: GPL-2 | GPL-3
LazyLoad: yes
Depends: limma, crmn, gplots, R (>= 3.1.0)
Packaged: 2014-12-29 18:19:26 UTC; alyshad
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-29 19:25:29

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New package forestplot with initial version 1.0
Package: forestplot
Version: 1.0
Date: 2014-12-29
Title: Advanced Forest Plot Using 'grid' Graphics
Authors@R: c(person(given = "Max", family = "Gordon", role = c("aut", "cre"), email = "max@gforge.se"), person(given = "Thomas", family = "Lumley", role = c("aut", "ctb")))
Description: The plot allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. The aim is to extend the use of forest plots beyond meta-analyses. This is a more general version of the original 'rmeta' package's forestplot function and relies heavily on the 'grid' package.
License: GPL-2
URL: http://gforge.se/packages/
BugReports: https://github.com/gforge/forestplot/issues
Biarch: yes
Depends: grid
Suggests: testthat, knitr
Encoding: UTF-8
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2014-12-29 18:28:15 UTC; Max
Author: Max Gordon [aut, cre], Thomas Lumley [aut, ctb]
Maintainer: Max Gordon
Repository: CRAN
Date/Publication: 2014-12-30 00:24:56

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New package CORE with initial version 3.0
Package: CORE
Type: Package
Title: Cores of Recurrent Events
Version: 3.0
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun
Description: given a collection of intervals with integer start and end positions, find recurrently targeted regions and estimate the significance of finding. Randomization is implemented by parallel methods, either using local host machines, or submitting grid engine jobs.
License: GPL-2
Imports: parallel
Packaged: 2014-12-15 18:58:56 UTC; gsun
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-30 00:12:08

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New package TBEST with initial version 5.0
Package: TBEST
Type: Package
Title: Tree Branches Evaluated Statistically for Tightness
Version: 5.0
Date: 2014-10-30
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
License: GPL-2
Depends: parallel, signal, fdrtool
Packaged: 2014-12-17 18:08:14 UTC; gsun
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-29 17:56:43

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Package ecolMod updated to version 1.2.6 with previous version 1.2.5 dated 2014-01-13

Title: "A practical guide to ecological modelling - using R as a simulation platform"
Description: Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer. All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11. The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter. Solutions to model projects are in the same subdirectories.
Author: Karline Soetaert , Peter MJ Herman
Maintainer: Karline Soetaert

Diff between ecolMod versions 1.2.5 dated 2014-01-13 and 1.2.6 dated 2014-12-29

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Package dupiR updated to version 1.2 with previous version 1.1 dated 2013-08-06

Title: Bayesian inference from count data using discrete uniform priors
Description: Inference of population sizes using a binomial likelihood and least informative discrete uniform priors.
Author: Federico Comoglio and Maurizio Rinaldi
Maintainer: Federico Comoglio

Diff between dupiR versions 1.1 dated 2013-08-06 and 1.2 dated 2014-12-29

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New package BANFF with initial version 0.1
Package: BANFF
Type: Package
Title: Bayesian Network Feature Finder
Version: 0.1
Description: Provides efficient Bayesian nonparametric models for network feature selection
Depends: foreach, doParallel
License: GPL-2
Imports: DPpackage, igraph, mclust, pscl, tmvtnorm, network
Packaged: 2014-12-29 14:49:59 UTC; Zhou Lan
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-29 17:50:58

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Package raters updated to version 2.0.1 with previous version 2.0 dated 2014-12-24

Title: A Modification of Fleiss' Kappa in Case of Nominal and Ordinal Variables
Description: The kappa statistic implemented by Fleiss is a very popular index for assessing the reliability of agreement among multiple observers. It is used both in the psychological and in the psychiatric field. Other fields of application are typically medicine, biology and engineering. Unfortunately,the kappa statistic may behave inconsistently in case of strong agreement between raters, since this index assumes lower values than it would have been expected. We propose a modification kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo simulations are used both to testing statistical hypotheses and to calculating percentile bootstrap confidence intervals based on proposed statistic in case of nominal and ordinal data.
Author: Daniele Giardiello [cre], Piero Quatto [aut], Enrico Ripamonti [aut], Stefano Vigliani [ctb]
Maintainer: Daniele Giardiello

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Package usl updated to version 1.4.1 with previous version 1.4.0 dated 2014-11-04

Title: Analyze System Scalability with the Universal Scalability Law
Description: The Universal Scalability Law is a model to predict hardware and software scalability. It uses system capacity as a function of load to forecast the scalability for the system.
Author: Neil J. Gunther [aut], Stefan Moeding [aut, cre]
Maintainer: Stefan Moeding

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Package selectiongain updated to version 2.0.40 with previous version 2.0.29 dated 2013-12-11

Title: A tool for calculation and optimization of the expected gain from multi-stage selection
Description: Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
Author: Xuefei Mi, H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi

Diff between selectiongain versions 2.0.29 dated 2013-12-11 and 2.0.40 dated 2014-12-29

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Package RObsDat updated to version 14.12 with previous version 14.04 dated 2014-05-07

Title: Data Mangement for Hydrology and Beyond Using the Observations Data Model
Description: RObsDat is designed to support data management in hydrology and other fields. It provides functions to enter and modify your data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser

Diff between RObsDat versions 14.04 dated 2014-05-07 and 14.12 dated 2014-12-29

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Package PReMiuM updated to version 3.0.32 with previous version 3.0.30 dated 2014-09-12

Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.
Author: David I. Hastie , Silvia Liverani and Sylvia Richardson with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi
Maintainer: Silvia Liverani

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Package OceanView updated to version 1.0.2 with previous version 1.0.1 dated 2014-08-14

Title: Visualisation of Oceanographic Data and Model Output.
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Author: Karline Soetaert
Maintainer: Karline Soetaert

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Package diffEq updated to version 1.0-1 with previous version 1.0 dated 2012-04-19

Title: Functions from the book Solving Differential Equations in R
Description: Functions and examples from the book Solving Differential Equations in R by Karline Soetaert, Jeff R Cash and Francesca Mazzia. Springer, 2012.
Author: Karline Soetaert
Maintainer: Karline Soetaert

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Package R4CDISC updated to version 0.3 with previous version 0.2 dated 2014-05-18

Title: Read CDISC Data Files
Description: CDISC Dataset-XML and Define-XML are used as file format for clinical trial data and metadata respectively. This functions supports reading both Dataset-XML and Define-XML.
Author: Ippei Akiya
Maintainer: Ippei Akiya

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 R4CDISC-0.2/R4CDISC/inst/extdata/suppcm.xml                                    |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppdm.xml                                    |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppeg.xml                                    |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppex.xml                                    |only
 R4CDISC-0.2/R4CDISC/inst/extdata/supplb.xml                                    |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppqscg.xml                                  |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppqscs.xml                                  |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppqsmm.xml                                  |only
 R4CDISC-0.2/R4CDISC/inst/extdata/suppvs.xml                                    |only
 R4CDISC-0.2/R4CDISC/inst/extdata/sv.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/extdata/ta.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/extdata/te.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/extdata/ti.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/extdata/ts.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/extdata/tv.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/extdata/vs.xml                                        |only
 R4CDISC-0.2/R4CDISC/inst/tests/test-define-xml.R                               |only
 R4CDISC-0.3/R4CDISC/DESCRIPTION                                                |   12 -
 R4CDISC-0.3/R4CDISC/MD5                                                        |  103 +++++-----
 R4CDISC-0.3/R4CDISC/NAMESPACE                                                  |    3 
 R4CDISC-0.3/R4CDISC/R/getAttr.R                                                |    2 
 R4CDISC-0.3/R4CDISC/R/getCT.R                                                  |only
 R4CDISC-0.3/R4CDISC/R/getCodeListItem.R                                        |only
 R4CDISC-0.3/R4CDISC/R/getCodeListRef.R                                         |only
 R4CDISC-0.3/R4CDISC/R/getEnumeratedItem.R                                      |only
 R4CDISC-0.3/R4CDISC/R/getItemDef.R                                             |   26 +-
 R4CDISC-0.3/R4CDISC/R/getOrigin.R                                              |only
 R4CDISC-0.3/R4CDISC/R/getVal.R                                                 |    4 
 R4CDISC-0.3/R4CDISC/R/namespaces.R                                             |only
 R4CDISC-0.3/R4CDISC/inst/extdata/ADaM                                          |only
 R4CDISC-0.3/R4CDISC/inst/extdata/SDTM                                          |only
 R4CDISC-0.3/R4CDISC/inst/tests/test-adam-define-xml.R                          |only
 R4CDISC-0.3/R4CDISC/inst/tests/test-dataset-xml.R                              |    5 
 R4CDISC-0.3/R4CDISC/inst/tests/test-sdtm-define-xml.R                          |only
 R4CDISC-0.3/R4CDISC/man/getCT.Rd                                               |only
 R4CDISC-0.3/R4CDISC/man/getDLMD.Rd                                             |    3 
 R4CDISC-0.3/R4CDISC/man/getValMD.Rd                                            |    3 
 R4CDISC-0.3/R4CDISC/man/getVarMD.Rd                                            |    5 
 R4CDISC-0.3/R4CDISC/man/read.dataset.xml.Rd                                    |    5 
 59 files changed, 101 insertions(+), 70 deletions(-)

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Package countrycode updated to version 0.18 with previous version 0.17 dated 2014-07-15

Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of eleven coding schemes, convert between coding schemes, and assign region descriptors.
Author: Vincent Arel-Bundock
Maintainer: Vincent Arel-Bundock

Diff between countrycode versions 0.17 dated 2014-07-15 and 0.18 dated 2014-12-29

 countrycode-0.17/countrycode/man/countrycode_test.Rd    |only
 countrycode-0.18/countrycode/DESCRIPTION                |   16 ++--
 countrycode-0.18/countrycode/MD5                        |   21 ++---
 countrycode-0.18/countrycode/NAMESPACE                  |    2 
 countrycode-0.18/countrycode/NEWS                       |    7 +
 countrycode-0.18/countrycode/R/countrycode-package.R    |    2 
 countrycode-0.18/countrycode/R/countrycode.R            |   59 +---------------
 countrycode-0.18/countrycode/R/countrycode_data.R       |    2 
 countrycode-0.18/countrycode/data/countrycode_data.rda  |binary
 countrycode-0.18/countrycode/man/countrycode-package.Rd |    5 -
 countrycode-0.18/countrycode/man/countrycode.Rd         |    7 +
 countrycode-0.18/countrycode/man/countrycode_data.Rd    |    5 -
 12 files changed, 45 insertions(+), 81 deletions(-)

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Package tableone updated to version 0.6.3 with previous version 0.6.2 dated 2014-06-02

Title: Create "Table 1" to describe baseline characteristics
Description: This package creates "Table 1", i.e., description of baseline patient characteristics, which is essential in every medical research. This package provides functions to create such summaries for continuous and categorical variables, optionally with subgroup comparisons. The package was inspired by and based on descriptive statistics functions in Deducer, a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida

Diff between tableone versions 0.6.2 dated 2014-06-02 and 0.6.3 dated 2014-12-29

 DESCRIPTION              |   11 ++++++-----
 MD5                      |   33 +++++++++++++++++++--------------
 NAMESPACE                |    2 +-
 NEWS                     |   10 +++++++++-
 build                    |only
 inst                     |only
 man/CreateCatTable.Rd    |    3 ++-
 man/CreateContTable.Rd   |    3 ++-
 man/CreateTableOne.Rd    |   19 ++++++++++---------
 man/ShowRegTable.Rd      |    3 ++-
 man/print.CatTable.Rd    |    3 ++-
 man/print.ContTable.Rd   |    3 ++-
 man/print.TableOne.Rd    |    3 ++-
 man/summary.CatTable.Rd  |    3 ++-
 man/summary.ContTable.Rd |    3 ++-
 man/summary.TableOne.Rd  |    3 ++-
 man/tableone-package.Rd  |    3 ++-
 vignettes                |only
 18 files changed, 65 insertions(+), 40 deletions(-)

More information about tableone at CRAN
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Package easingr (with last version 1.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-09-02 1.0.1
2014-06-28 1.0.0

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