Mon, 11 Jan 2016

Package rodd updated to version 0.2-1 with previous version 0.1-1 dated 2014-12-13

Title: Optimal Discriminating Designs
Description: A collection of functions for numerical construction of optimal discriminating designs. At the current moment T-optimal designs (which maximize the lower bound for the power of F-test for regression model discrimination), KL-optimal designs (for lognormal errors) and their robust analogues can be calculated with the package.
Author: Roman Guchenko [aut, cre]
Maintainer: Roman Guchenko <RomanGuchenko@yandex.ru>

Diff between rodd versions 0.1-1 dated 2014-12-13 and 0.2-1 dated 2016-01-11

 DESCRIPTION                       |    9 +--
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Package networkDynamicData updated to version 0.2.1 with previous version 0.1.0 dated 2014-02-07

Title: Dynamic (Longitudinal) Network Datasets
Description: A collection of dynamic network data sets from various sources and multiple authors represented as 'networkDynamic'-formatted objects.
Author: Skye Bender-deMoll [cre], Martina Morris [ctb], Li Wang [ctb], Gerhard van de Bunt [ctb], Goele Bossaert [ctb], Nadine Meidert [ctb], SocioPatterns.org [ctb], Tore Opsahi [ctb], Radoslaw Michalski, (et al) [ctb], Allison Davis, (et. al.) [ctb], C.E. Priebe, (et. al.) [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>

Diff between networkDynamicData versions 0.1.0 dated 2014-02-07 and 0.2.1 dated 2016-01-11

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Package mixtools updated to version 1.0.4 with previous version 1.0.3 dated 2015-04-19

Title: Tools for Analyzing Finite Mixture Models
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre], Tatiana Benaglia [aut], Didier Chauveau [aut], David Hunter [aut], Ryan Elmore [ctb], Thomas Hettmansperger [ctb], Hoben Thomas [ctb], Fengjuan Xuan [ctb]
Maintainer: Derek Young <derek.young@uky.edu>

Diff between mixtools versions 1.0.3 dated 2015-04-19 and 1.0.4 dated 2016-01-11

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Package mefa updated to version 3.2-7 with previous version 3.2-6 dated 2015-11-22

Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>

Diff between mefa versions 3.2-6 dated 2015-11-22 and 3.2-7 dated 2016-01-11

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Package rpdo updated to version 0.1.1 with previous version 0.1.0 dated 2015-10-19

Title: Pacific Decadal Oscillation Index
Description: Monthly Pacific Decadal Oscillation (PDO) index values from January 1900 to present.
Author: Joe Thorley [aut, cre], Nathan Mantua [aut, dtc], Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between rpdo versions 0.1.0 dated 2015-10-19 and 0.1.1 dated 2016-01-11

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New package ontologyPlot with initial version 1.0
Package: ontologyPlot
Type: Package
Title: Functions for Visualising Sets of Ontological Terms
Version: 1.0
Date: 2016-01-11
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Description: Functions for visualising sets of ontological terms using the graphviz layout system.
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Imports: ontologyIndex, Rgraphviz, methods, functional, magrittr
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-01-11 17:11:40 UTC; dg333
Repository: CRAN
Date/Publication: 2016-01-11 21:18:43

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New package LPR with initial version 1.0
Package: LPR
Type: Package
Title: Lasso and Partial Ridge
Version: 1.0
Date: 2016-01-10
Author: Hanzhong Liu, Xin Xu, Jingyi Jessica Li, Bin Yu*
Maintainer: Xin Xu <xin.xu@yale.edu>
Imports: glmnet,slam,parallel,foreach,iterators,doParallel,lattice,Matrix
Description: Contains a function called "LPR" to estimate coefficients using Lasso and Partial Ridge method and to calculate confidence intervals through bootstrap.
License: GNU General Public License version 2
NeedsCompilation: no
Packaged: 2016-01-11 17:16:50 UTC; xin
Repository: CRAN
Date/Publication: 2016-01-11 21:18:39

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Package gSEM updated to version 0.4.3.4 with previous version 0.4.3.3 dated 2015-12-23

Title: Semi-Supervised Generalized Structural Equation Modeling
Description: Conducts a semi-gSEM statistical analysis (semi-supervised generalized structural equation modeling) on a data frame of coincident observations of multiple predictive or intermediate variables and a final continuous, outcome variable, via two functions sgSEMp1() and sgSEMp2(), representing fittings based on two statistical principles. Principle 1 determines all sensible univariate relationships in the spirit of the Markovian process. The relationship between each pair of variables, including predictors and the final outcome variable, is determined with the Markovian property that the value of the current predictor is sufficient in relating to the next level variable, i.e., the relationship is independent of the specific value of the preceding-level variables to the current predictor, given the current value. Principle 2 resembles the multiple regression principle in the way multiple predictors are considered simultaneously. Specifically, the relationship of the first-level predictors (such as Time and irradiance etc) to the outcome variable (such as, module degradation or yellowing) is fit by a supervised additive model. Then each significant intermediate variable is taken as the new outcome variable and the other variables (except the final outcome variable) as the predictors in investigating the next-level multivariate relationship by a supervised additive model. This fitting process is continued until all sensible models are investigated.
Author: Junheng Ma <jxm216@case.edu>, Nicholas Wheeler <nrw16@case.edu>, Yifan Xu <ethan.yifanxu@case.edu>, Wenyu Du <wxd97@case.edu>, Abdulkerim Gok <axg515@case.edu>, Jiayang Sun <jiayang.sun@case.edu>
Maintainer: Junheng Ma <jxm216@case.edu>

Diff between gSEM versions 0.4.3.3 dated 2015-12-23 and 0.4.3.4 dated 2016-01-11

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New package gsEasy with initial version 1.0
Package: gsEasy
Type: Package
Title: Gene Set Enrichment Analysis in R
Version: 1.0
Date: 2016-01-11
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Description: R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005).
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.2), ontologyIndex
LinkingTo: Rcpp
Depends: R (>= 3.0.0)
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-01-11 17:48:59 UTC; dg333
Repository: CRAN
Date/Publication: 2016-01-11 21:18:42

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Package pRF updated to version 1.2 with previous version 1.1 dated 2015-11-05

Title: Permutation Significance for Random Forests
Description: Estimate False Discovery Rates (FDRs) for importance metrics from random forest runs.
Author: Ankur Chakravarthy
Maintainer: Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>

Diff between pRF versions 1.1 dated 2015-11-05 and 1.2 dated 2016-01-11

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Package ggsubplot (with last version 0.3.2) was removed from CRAN

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

2013-12-13 0.3.2
2013-11-26 0.3.1

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Package urca updated to version 1.2-9 with previous version 1.2-8 dated 2013-06-06

Title: Unit Root and Cointegration Tests for Time Series Data
Description: Unit root and cointegration tests encountered in applied econometric analysis are implemented.
Author: Bernhard Pfaff [aut, cre], Eric Zivot [ctb], Matthieu Stigler [ctb]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>

Diff between urca versions 1.2-8 dated 2013-06-06 and 1.2-9 dated 2016-01-11

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New package ontologyIndex with initial version 1.0
Package: ontologyIndex
Type: Package
Title: Functions for Reading Ontologies into R
Version: 1.0
Date: 2016-01-11
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Description: Functions for reading ontologies into R as lists and handling sets of ontological terms.
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-01-11 14:16:58 UTC; dg333
Repository: CRAN
Date/Publication: 2016-01-11 15:32:37

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Package lgcp updated to version 1.3-14 with previous version 1.3-13 dated 2015-11-19

Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional code contributions from Edzer Pebesma.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>

Diff between lgcp versions 1.3-13 dated 2015-11-19 and 1.3-14 dated 2016-01-11

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Package cruts updated to version 0.2 with previous version 0.1 dated 2015-07-11

Title: Interface to Climatic Research Unit Time-Series Version 3.21 Data
Description: Functions for reading in and manipulating CRU TS3.21: Climatic Research Unit (CRU) Time-Series (TS) Version 3.21 data.
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>

Diff between cruts versions 0.1 dated 2015-07-11 and 0.2 dated 2016-01-11

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Package telegram updated to version 0.4.0 with previous version 0.3.0 dated 2015-12-29

Title: R Wrapper Around the Telegram Bot API
Description: R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to access Telegram's messaging facilities with ease (e.g. you send messages, images, files from R to your smartphone).
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>

Diff between telegram versions 0.3.0 dated 2015-12-29 and 0.4.0 dated 2016-01-11

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Package rlm updated to version 1.2 with previous version 1.1 dated 2015-02-21

Title: Robust Fitting of Linear Model
Description: Robust fitting of linear model which can take response in matrix form.
Author: Oleg Yegorov <egorov@smedx.com>
Maintainer: Oleg Yegorov <egorov@smedx.com>

Diff between rlm versions 1.1 dated 2015-02-21 and 1.2 dated 2016-01-11

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Package ncdf (with last version 1.6.9) was removed from CRAN

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

2015-11-29 1.6.9
2014-08-25 1.6.8
2014-06-16 1.6.7
2011-09-02 1.6.6
2011-01-10 1.6.5
2010-07-30 1.6.2
2010-07-30 1.6.3
2010-05-17 1.6.1
2006-07-10 1.6

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Package soilphysics updated to version 3.0 with previous version 2.4 dated 2015-06-26

Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>

Diff between soilphysics versions 2.4 dated 2015-06-26 and 3.0 dated 2016-01-11

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Package RNeo4j updated to version 1.6.2 with previous version 1.6.1 dated 2015-11-30

Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>

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Package reservoir updated to version 1.1.1 with previous version 1.1.0 dated 2016-01-04

Title: Tools for Analysis, Design, and Operation of Water Supply Storages
Description: Measure single-storage water supply system performance using resilience, reliability, and vulnerability metrics; assess storage-yield-reliability relationships; determine no-fail storage with sequent peak analysis; optimize release decisions for water supply, hydropower, and multi-objective reservoirs using deterministic and stochastic dynamic programming; evaluate inflow persistence using the Hurst coefficient.
Author: Sean Turner [aut, cre], Jia Yi Ng [aut], Stefano Galelli [aut]
Maintainer: Sean Turner <swd.turner@gmail.com>

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Package quanteda updated to version 0.9.2-0 with previous version 0.9.0-1 dated 2015-11-27

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre], Paul Nulty [aut], Pablo Barberá [ctb], Kohei Watanabe [ctb], Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package prcbench updated to version 0.2.0 with previous version 0.1.0 dated 2016-01-08

Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating Precision-Recall curves under various conditions.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between prcbench versions 0.1.0 dated 2016-01-08 and 0.2.0 dated 2016-01-11

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Package PhySortR updated to version 1.0.5 with previous version 1.0.3 dated 2015-12-21

Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non- Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port), Debashish Bhattacharya [aut], Mark Ragan [aut], Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>

Diff between PhySortR versions 1.0.3 dated 2015-12-21 and 1.0.5 dated 2016-01-11

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Package nparACT updated to version 0.2 with previous version 0.1 dated 2015-10-22

Title: Non-Parametric Measures of Actigraphy Data
Description: Computes interday stability (IS), intraday variability (IV) & the relative amplitude (RA) from actigraphy data as described in van Someren et al. (1999). Additionally, it also computes L5 (i.e. the 5 hours with lowest average actigraphy amplitude) and M10 (the 10 hours with highest average amplitude) as well as the respective start times. The flex versions will also compute the L-value for a user-defined number of minutes. IS describes the strength of coupling of a rhythm to supposedly stable zeitgebers. It varies between 0 (Gaussian Noise) and 1 for perfect IS. IV describes the fragmentation of a rhythm, i.e. the frequency and extent of transitions between rest and activity. It is near 0 for a perfect sine wave, about 2 for Gaussian noise and may be even higher when a definite ultradian period of about 2 hrs is present. RA is the relative amplitude of a rhythm. Note that to obtain reliable results, actigraphy data should cover a reasonable number of days.
Author: Christine Blume <christine.blume@sbg.ac.at> Nayantara Santhi <n.santhi@surrey.ac.uk> Manuel Schabus <manuel.schabus@sbg.ac.at>
Maintainer: Christine Blume <christine.blume@sbg.ac.at>

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New package mmppr with initial version 0.1
Package: mmppr
Version: 0.1
Date: 2016-01-06
Title: Markov Modulated Poisson Process for Unsupervised Event Detection in Time Series of Counts
Author: Graham Mueller [aut, cre]
Maintainer: Peter Landwehr <peter.landwehr@giantoak.com>
Depends: R (>= 3.0.2), expm, reshape2, stats, methods
Description: Time-series of count data occur in many different contexts. A Markov-modulated Poisson process provides a framework for detecting anomalous events using an unsupervised learning approach.
License: GPL (>= 2)
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-01-11 09:44:41

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New package concordance with initial version 1.6
Package: concordance
Type: Package
Title: Product Concordance
Version: 1.6
Date: 2016-01-05
Author: Feng Zhu, In Song Kim
Maintainer: In Song Kim <insong@mit.edu>
Description: A set of utilities for matching products in different classification codes used in international trade research. It supports concordance between HS (Combined), ISIC Rev. 2,3, and SITC1,2,3,4 product classification codes, as well as BEC, NAICS, and SIC classifications. It also provides code nomenclature / descriptions look-up, Rauch classification look-up (via concordance to SITC2) and trade elasticity look-up (via concordance to SITC2/3 or HS3.ss).
License: GPL-2
Depends: R (>= 2.10.1)
LazyData: true
NeedsCompilation: no
Packaged: 2016-01-11 04:06:36 UTC; insong
Repository: CRAN
Date/Publication: 2016-01-11 09:44:39

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Package ARTool updated to version 0.10.0 with previous version 0.9.5 dated 2015-06-01

Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric factorial ANOVAs as described by J. O. Wobbrock, L. Findlater, D. Gergle, & J. J. Higgins, "The Aligned Rank Transform for nonparametric factorial analyses using only ANOVA procedures", CHI 2011.
Author: Matthew Kay [aut, cre], Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>

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