Sat, 01 Nov 2014

New package RealVAMS with initial version 0.3-1
Package: RealVAMS
Type: Package
Title: Multivariate VAM Fitting
Version: 0.3-1
Date: 2014-09-25
Author: Andrew Karl, Jennifer Broatch, and Jennifer Green
Maintainer: Andrew Karl
Description: The RealVAMs package fits a multivariate value-added model (VAM) (see Broatch and Lohr 2012) with normally distributed test scores and a binary outcome indicator. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
License: GPL-2
Depends: R (>= 3.0.0), Matrix
Imports: numDeriv, Rcpp (>= 0.10.6)
LazyData: yes
ByteCompile: yes
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2014-11-01 03:36:55 UTC; Andrew
Repository: CRAN
Date/Publication: 2014-11-01 07:19:08

More information about RealVAMS at CRAN
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Fri, 31 Oct 2014

Package VNM updated to version 2.0 with previous version 1.0 dated 2014-05-16

Title: Using V-algorithm and Newton-Raphson Method to Obtain Multiple-objective Optimal Design
Description: Using V-algorithm and Newton-Raphson method to obtain multiple-objective optimal design for estimating the shape of dose-response, the ED50 (the dose producing an effect mid-way between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 4-parameter logistic model and for evaluating its efficiencies for the three objectives.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang

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More information about VNM at CRAN
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Package vcdExtra updated to version 0.6-3 with previous version 0.6-1 dated 2014-06-10

Title: vcd extensions and additions
Description: Provides additional data sets, methods and documentation to complement the vcd package for Visualizing Categorical Data and the gnm package for Generalized Nonlinear Models. In particular, vcdExtra extends mosaic, assoc and sieve plots from vcd to handle glm() and gnm() models and adds a 3D version in mosaic3d. Additionally, methods are provided for comparing and visualizing lists of glm and loglm objects.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly

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Package texreg updated to version 1.34 with previous version 1.33 dated 2014-07-21

Title: Conversion of R regression output to LaTeX or HTML tables.
Description: texreg converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld

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Package statar updated to version 0.1.2 with previous version 0.1.1 dated 2014-10-26

Title: Tools Inspired by Stata to Clean, Explore and Join Datasets
Description: statar makes it easier to work with tabular datasets. The package includes a set of functions to clean and summarize variables, to join datasets using an SQL-syntax, to manipulate datasets with a panel structure (elapsed dates, lead/lag, rolling functions, fill in missing values based on previous dates, add rows for missing dates). The package also includes functions to emulate Stata and Julia string and expression interpolation. statar is based on the data.table package and is inspired by Stata.
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez

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Package Crossover updated to version 0.1-13 with previous version 0.1-12 dated 2014-09-25

Title: Crossover Designs
Description: Package Crossover provides different crossover designs from combinatorial or search algorithms as well as from literature and a GUI to access them.
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer

Diff between Crossover versions 0.1-12 dated 2014-09-25 and 0.1-13 dated 2014-10-31

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Package seqinr updated to version 3.0-9 with previous version 3.0-7 dated 2012-12-13

Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data management under the ACNUC system.
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel and Guy Perriere
Maintainer: Simon Penel

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Package SKAT updated to version 1.0 with previous version 0.95 dated 2014-02-18

Title: SNP-set (Sequence) Kernel Association Test
Description: SKAT is a kernel regression based association test between a set of single nucleotide polymorphism (SNP) and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, while adjusting for covariates, such as principal components to account for population stratification.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee

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Package PrivateLR updated to version 1.2-21 with previous version 1.1-69 dated 2013-06-04

Title: Differentially Private Regularized Logistic Regression
Description: PrivateLR implements two differentially private algorithms for estimating L2-regularized logistic regression coefficients. A randomized algorithm F is epsilon-differentially private (C. Dwork, Differential Privacy, ICALP 2006), if |log(P(F(D) in S)) - log(P(F(D') in S))| <= epsilon for any pair D, D' of datasets that differ in exactly one element, any set S, and the randomness is taken over the choices F makes.
Author: Staal A. Vinterbo
Maintainer: Staal A. Vinterbo

Diff between PrivateLR versions 1.1-69 dated 2013-06-04 and 1.2-21 dated 2014-10-31

 DESCRIPTION |   18 ++++++----
 MD5         |    6 +--
 R/dplr.r    |  106 +++++++++++++++++++++++++++++-------------------------------
 man/dplr.Rd |   80 +++++++++++++++++++++++++++++++++++----------
 4 files changed, 130 insertions(+), 80 deletions(-)

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New package hermite with initial version 1.0
Package: hermite
Type: Package
Title: Generalized Hermite distribution
Version: 1.0
Date: 2014-10-30
Encoding: UTF-8
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler
Description: Probability functions for the generalized Hermite distribution
Depends: R (>= 2.15.0)
Repository: CRAN
License: GPL (>= 2)
Packaged: 2014-10-31 15:08:23 UTC; dmorinya
NeedsCompilation: no
Date/Publication: 2014-10-31 16:16:01

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Package TR8 updated to version 0.9.11 with previous version 0.9 dated 2014-10-28

Title: A tool for downloading functional traits data for plant species
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.
Author: Gionata Bocci
Maintainer: Gionata Bocci

Diff between TR8 versions 0.9 dated 2014-10-28 and 0.9.11 dated 2014-10-31

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 20 files changed, 43 insertions(+), 41 deletions(-)

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Package rex updated to version 0.1.2 with previous version 0.1.1 dated 2014-10-20

Title: Friendly regular expressions
Description: A more friendly, human-readable interface for the construction of regular expressions.
Author: Kevin Ushey [aut], Jim Hester [cre, aut]
Maintainer: Jim Hester

Diff between rex versions 0.1.1 dated 2014-10-20 and 0.1.2 dated 2014-10-31

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 6 files changed, 30 insertions(+), 10 deletions(-)

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Package BatchExperiments updated to version 1.4 with previous version 1.3 dated 2014-09-24

Title: Statistical experiments on batch computing clusters.
Description: Extends the BatchJobs package to run statistical experiments on batch computing clusters. For further details see the project web page.
Author: Bernd Bischl , Michel Lang , Olaf Mersmann
Maintainer: Michel Lang

Diff between BatchExperiments versions 1.3 dated 2014-09-24 and 1.4 dated 2014-10-31

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 6 files changed, 33 insertions(+), 16 deletions(-)

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Package STARSEQ (with last version 1.2.1) was removed from CRAN

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

2014-10-21 1.2.1
2012-08-24 1.02

Permanent link
Package highriskzone (with last version 1.1) was removed from CRAN

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

2014-02-20 1.1
2012-12-18 1.0

Permanent link
Package tuple updated to version 0.4-02 with previous version 0.4-01 dated 2014-08-22

Title: Find every match, or orphan, duplicate, triplicate, or other replicated values
Description: Functions to find all matches or non-matches, orphans, and duplicate or other replicated elements.
Author: Emmanuel Lazaridis [aut, cre]
Maintainer: Emmanuel Lazaridis

Diff between tuple versions 0.4-01 dated 2014-08-22 and 0.4-02 dated 2014-10-31

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More information about tuple at CRAN
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Package laGP updated to version 1.1-3 with previous version 1.1-2 dated 2014-10-17

Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy

Diff between laGP versions 1.1-2 dated 2014-10-17 and 1.1-3 dated 2014-10-31

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More information about laGP at CRAN
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Thu, 30 Oct 2014

Package qtl updated to version 1.34-17 with previous version 1.34-16 dated 2014-10-29

Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman

Diff between qtl versions 1.34-16 dated 2014-10-29 and 1.34-17 dated 2014-10-30

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Package dynBiplotGUI updated to version 1.1.1 with previous version 1.1.0 dated 2014-06-27

Title: Full Interactive GUI for Dynamic Biplot in R
Description: A GUI to solve Dynamic Biplots, classic Biplot and HJ-biplot. Try matrices of 2-way and 3-way. Multilanguage.
Author: Jaime Egido [aut, cre]
Maintainer: Jaime Egido

Diff between dynBiplotGUI versions 1.1.0 dated 2014-06-27 and 1.1.1 dated 2014-10-30

 ChangeLog                   |   13 ++++
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Package BatchJobs updated to version 1.5 with previous version 1.4 dated 2014-09-24

Title: Batch computing with R.
Description: Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.
Author: Bernd Bischl , Michel Lang
Maintainer: Bernd Bischl

Diff between BatchJobs versions 1.4 dated 2014-09-24 and 1.5 dated 2014-10-30

 DESCRIPTION                         |   14 +++----
 MD5                                 |   68 ++++++++++++++++++------------------
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Package rNOMADS updated to version 2.0.4 with previous version 2.0.3 dated 2014-10-13

Title: An interface to the NOAA Operational Model Archive and Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman

Diff between rNOMADS versions 2.0.3 dated 2014-10-13 and 2.0.4 dated 2014-10-30

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Package mapplots updated to version 1.5 with previous version 1.4 dated 2013-07-15

Title: Data Visualisation on Maps
Description: Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.
Author: Hans Gerritsen
Maintainer: Hans Gerritsen

Diff between mapplots versions 1.4 dated 2013-07-15 and 1.5 dated 2014-10-30

 DESCRIPTION             |    8 +++----
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New package genpathmox with initial version 0.1
Package: genpathmox
Title: Generalized PATHMOX Algorithm for PLS-PM, LS and LAD Regression
Version: 0.1
Authors@R: "Giuseppe Lamberti [aut, cre]"
Description: genpathmox provides a very interesting solution for handling segmentation variables in complex statistical methodology. It contains en extended version of the PATHMOX algorithm in the context of partial least square path modeling (Sanchez, 2009) including the F-block test (to detect the responsible latent endogenous equations of the difference), the F-coefficient (to detect the path coefficients responsible of the difference) and the invariance test (to realize a comparison between the sub-models' latent variables). Furthermore, the package contains a generalized version of the PATHMOX algorithm to approach different methodologies: linear regression and least absolute regression models.
Depends: R (>= 3.1.1),plspm, quantreg,mice,diagram, methods
License: GPL-3
LazyData: true
Packaged: 2014-10-30 14:37:42 UTC; giuseppelamberti
Author: "Giuseppe Lamberti" [aut, cre]
Maintainer: "Giuseppe Lamberti"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 19:35:26

More information about genpathmox at CRAN
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Package BBmisc updated to version 1.8 with previous version 1.7 dated 2014-06-21

Title: Miscellaneous helper functions for B. Bischl.
Description: Miscellaneous helper functions for and from B. Bischl and some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl [aut, cre], Michel Lang [aut], Jakob Bossek [aut], Daniel Horn [aut], Jakob Richter [aut]
Maintainer: Bernd Bischl

Diff between BBmisc versions 1.7 dated 2014-06-21 and 1.8 dated 2014-10-30

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More information about BBmisc at CRAN
Permanent link

Package Rcmdr updated to version 2.1-4 with previous version 2.1-3 dated 2014-10-09

Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Milan Bouchet-Valat [aut], Liviu Andronic [ctb], Michael Ash [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter Wolf [ctb], Kevin Wright [ctb]
Maintainer: John Fox

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More information about Rcmdr at CRAN
Permanent link

Package hglm updated to version 2.0-11 with previous version 2.0-9 dated 2014-09-27

Title: Hierarchical Generalized Linear Models
Description: This package fits hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Xia Shen, Moudud Alam, Lars Ronnegard
Maintainer: Xia Shen

Diff between hglm versions 2.0-9 dated 2014-09-27 and 2.0-11 dated 2014-10-30

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Permanent link

Package surveillance updated to version 1.8-1 with previous version 1.8-0 dated 2014-06-17

Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Description: A package implementing statistical methods for the modeling and change-point detection in time series of counts, proportions and categorical data, as well as for the modeling of continuous-time epidemic phenomena, e.g. discrete-space setups such as the spatially enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for surveillance data, or continuous-space point process data such as the occurrence of disease or earthquakes. Main focus is on outbreak detection in count data time series originating from public health surveillance of infectious diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics or social sciences. Currently the package contains implementations of typical outbreak detection procedures such as Farrington et al (1996), Noufaily et al (2012) or the negative binomial LR-CUSUM method described in Hoehle and Paul (2008). Furthermore, inference methods for the retrospective infectious disease model in Held et al (2005), Held et al (2006), Paul et al (2008) and Paul and Held (2011) are provided. A novel CUSUM approach combining logistic and multinomial logistic modelling is also included. Continuous self-exciting spatio-temporal point processes are modeled through additive-multiplicative conditional intensities as described in Hhle (2009) ("twinSIR", discrete space) and Meyer et al (2012) ("twinstim", continuous space). The package contains several real-world data sets, the ability to simulate outbreak data, visualize the results of the monitoring in temporal, spatial or spatio-temporal fashion. Note: The suggested package INLA is unfortunately not available from any mainstream repository - in case one wants to use the 'boda' algorithm one needs to manually install the INLA package as specified at http://www.r-inla.org/download.
Author: Michael Hhle [aut, cre, ths], Sebastian Meyer [aut], Michaela Paul [aut], Leonhard Held [ctb, ths], Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb], Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabans Bov [ctb], Malle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb], Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)
Maintainer: Michael Hhle

Diff between surveillance versions 1.8-0 dated 2014-06-17 and 1.8-1 dated 2014-10-30

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More information about surveillance at CRAN
Permanent link

New package fPortfolio with initial version 3011.81
Package: fPortfolio
Title: Rmetrics - Portfolio Selection and Optimization
Date: 2014-10-30
Version: 3011.81
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz
Description: Environment for teaching "Financial Engineering and Computational Finance".
Depends: R (>= 2.15.1), methods, timeDate, timeSeries, fBasics, fAssets
Imports: fCopulae, robustbase, MASS, Rglpk, slam, Rsymphony, Rsolnp, kernlab, quadprog, rneos
Suggests: Rsocp, Rnlminb2, Rdonlp2, dplR, bcp, fGarch, mvoutlier
Additional_repositories: http://r-forge.r-project.org/
Note: SEVERAL PARTS ARE STILL PRELIMINARY AND MAY BE CHANGED IN THE FUTURE. THIS TYPICALLY INCLUDES FUNCTION AND ARGUMENT NAMES, AS WELL AS DEFAULTS FOR ARGUMENTS AND RETURN VALUES.
LazyData: yes
License: GPL (>= 2)
URL: https://www.rmetrics.org
Packaged: 2014-10-30 14:13:59 UTC; Tobi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 15:54:08

More information about fPortfolio at CRAN
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Package RcppArmadillo updated to version 0.4.500.0 with previous version 0.4.450.1.0 dated 2014-09-22

Title: Rcpp Integration for the Armadillo Templated Linear Algebra Library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The RcppArmadillo package includes the header files from the templated Armadillo library. Thus users do not need to install Armadillo itself in order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.4.450.1.0 dated 2014-09-22 and 0.4.500.0 dated 2014-10-30

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Package fAssets updated to version 3011.83 with previous version 3011.82 dated 2014-09-22

Title: Rmetrics - Analysing and Modelling Financial Assets
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz

Diff between fAssets versions 3011.82 dated 2014-09-22 and 3011.83 dated 2014-10-30

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More information about fAssets at CRAN
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Package etasFLP updated to version 1.1.1 with previous version 1.1.0 dated 2014-10-28

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

Diff between etasFLP versions 1.1.0 dated 2014-10-28 and 1.1.1 dated 2014-10-30

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Package sn updated to version 1.1-1 with previous version 1.1-0 dated 2014-08-04

Title: The skew-normal and skew-t distributions
Description: Define and manipulate probability distributions of the skew-normal family and some related ones (notably the skew-t family) and provide related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini

Diff between sn versions 1.1-0 dated 2014-08-04 and 1.1-1 dated 2014-10-30

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New package PrevMap with initial version 1.0
Package: PrevMap
Type: Package
Title: PrevMap - an R package for prevalence mapping
Version: 1.0
Date: 2014-06-25
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi
Depends: geoR, maxLik, raster, pdist
Description: The PrevMap package provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is also an extension of the 'geoR' package which should be installed first together with the 'maxLik', 'raster' and 'pdist' packages.
LazyData: true
License: GPL (>= 2)
Packaged: 2014-10-30 09:40:57 UTC; giorgi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 11:18:02

More information about PrevMap at CRAN
Permanent link

Package MortalitySmooth updated to version 2.3.3 with previous version 2.3.2 dated 2013-12-28

Title: Smoothing and Forecasting Poisson Counts with P-Splines
Description: Smoothing one- and two-dimensional Poisson counts with P-splines specifically tailored to mortality data. Extra-Poisson variation can be accounted as well as forecasting. Collection of mortality data and a specific function for selecting those data by country, sex, age and years.
Author: Carlo G Camarda
Maintainer: Carlo G Camarda

Diff between MortalitySmooth versions 2.3.2 dated 2013-12-28 and 2.3.3 dated 2014-10-30

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New package webutils with initial version 0.2
Package: webutils
Type: Package
Title: Utility Functions for Web Applications
Version: 0.2
Date: 2014-10-29
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: Utility functions for developing web applications. Includes parsers for application/x-www-form-urlencoded as well as multipart/form-data and examples of using the parser with either httpuv or rhttpd.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/webutils
BugReports: https://github.com/jeroenooms/webutils/issues
Imports: tools, utils, jsonlite
Suggests: httpuv
Packaged: 2014-10-30 00:32:01 UTC; jeroen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-30 07:46:54

More information about webutils at CRAN
Permanent link

Package pollstR updated to version 1.1.1 with previous version 1.1.0 dated 2014-08-18

Title: R client for the Huffpost Pollster API
Description: An R interface to the Huffington Post Pollster API, which provides programmatic interface to political polls.
Author: Jeffrey B. Arnold [aut, cre], Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold

Diff between pollstR versions 1.1.0 dated 2014-08-18 and 1.1.1 dated 2014-10-30

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Package multicon updated to version 1.3 with previous version 1.2 dated 2014-04-19

Title: Multivariate Constructs
Description: This packages includes functions designed to examine relationships among multivariate constructs.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman

Diff between multicon versions 1.2 dated 2014-04-19 and 1.3 dated 2014-10-30

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Wed, 29 Oct 2014

Package Taxonstand updated to version 1.5 with previous version 1.4 dated 2014-09-17

Title: Taxonomic standardization of plant species names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using the The Plant List (TPL) website (www.theplantlist.org)
Author: Luis Cayuela and Jari Oksanen
Maintainer: Luis Cayuela

Diff between Taxonstand versions 1.4 dated 2014-09-17 and 1.5 dated 2014-10-29

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New package exCon with initial version 0.1-0
Package: exCon
Type: Package
Title: Interactive Exploration of Contour Data
Version: 0.1-0
Date: 2014-10-29
Authors@R: c(person("Bryan", "Hanson", role = c("aut", "cre"), email = "hanson@depauw.edu"), person("Kristina", "Mulry", role = "ctb"))
Description: exCon is an interactive tool to explore topographic-like data sets. Such data sets take the form of a matrix in which the rows and columns provide location/frequency information, and the matrix elements contain altitude/response information. Such data is found in cartography, 2D spectroscopy and chemometrics. exCon creates an interactive web page showing the contoured data set along with slices from the original matrix parallel to each dimension. The page is written in d3/javascript.
License: GPL-3
Imports: jsonlite
URL: https://github.com/bryanhanson/exCon
ByteCompile: TRUE
BugReports: https://github.com/bryanhanson/exCon/issues
Depends: R (>= 3.0)
Packaged: 2014-10-29 19:41:42 UTC; bryanhanson
Author: Bryan Hanson [aut, cre], Kristina Mulry [ctb]
Maintainer: Bryan Hanson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 22:05:54

More information about exCon at CRAN
Permanent link

Package alm updated to version 0.3.1 with previous version 0.3.0 dated 2014-10-15

Title: R Client for the Lagotto Altmetrics API Platform.
Description: An R interface to the open source article level metrics API created by the Public Library of Science (PLOS). A number of publishers are using the open source app created by PLOS, so you can drop in a different base URL to the functions in this package to get to not only PLOS data, but data for Crossref, and more as the open source PLOS software is used. rCharts is in Enhances; and can be used for creating interactive charts (e.g., in the function plot_signposts in this package); obtain rCharts at https://github.com/ramnathv/rCharts.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut], Fenner Martin [aut]
Maintainer: Scott Chamberlain

Diff between alm versions 0.3.0 dated 2014-10-15 and 0.3.1 dated 2014-10-29

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Package R6 updated to version 2.0.1 with previous version 2.0 dated 2014-08-19

Title: Classes with reference semantics
Description: The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: "Winston Chang" [aut, cre]
Maintainer: "Winston Chang"

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Package qtl updated to version 1.34-16 with previous version 1.33-7 dated 2014-08-12

Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman

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Package isdals updated to version 2.0-4 with previous version 2.0-1 dated 2013-10-01

Title: Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
Description: Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
Author: Claus Ekstrom and Helle Sorensen
Maintainer: Claus Ekstrom

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Package fBasics updated to version 3011.87 with previous version 3010.86 dated 2013-05-01

Title: Rmetrics - Markets and Basic Statistics
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz

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Package ldr updated to version 1.3.3 with previous version 1.3.2 dated 2014-06-27

Title: Methods for likelihood-based dimension reduction in regression
Description: Functions, methods, and data sets for fitting likelihood-based dimension reduction in regression, using principal fitted components (pfc), likelihood acquired directions (lad), covariance reducing models (core).
Author: Kofi Placid Adragni, Andrew Raim
Maintainer: Kofi Placid Adragni

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Package HTSDiff updated to version 1.0.5 with previous version 1.0.2 dated 2014-07-28

Title: Differential Analysis of RNA-Seq Data with Poisson Mixture Models
Description: This package implements a Poisson mixture model to identify differentially expressed genes from RNA-seq data.
Author: Andrea Rau, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

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Package RSQLite.extfuns (with last version 0.0.1) was removed from CRAN

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

2010-05-30 0.0.1

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Package peacots updated to version 1.1 with previous version 1.0 dated 2014-06-05

Title: Periodogram Peaks in Correlated Time Series
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series.
Author: Stilianos Louca
Maintainer: Stilianos Louca

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Package pander updated to version 0.5.1 with previous version 0.5.0 dated 2014-10-28

Title: An R Pandoc Writer
Description: Contains some functions catching all messages, stdout and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in Pandoc's markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex Pandoc documents to e.g. HTML, PDF, docx or odt. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching backend.
Author: Gergely Daróczi , Roman Tsegelskyi
Maintainer: Gergely Daróczi

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Package nullabor updated to version 0.3.0 with previous version 0.2.1 dated 2012-07-23

Title: Tools for Graphical Inference
Description: Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.
Author: Hadley Wickham , Niladri Roy Chowdhury , Di Cook
Maintainer: Di Cook

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More information about nullabor at CRAN
Permanent link

New package DAMOCLES with initial version 1.0
Package: DAMOCLES
Type: Package
Title: Dynamic Assembly Model Of Colonization, Local Extinction and Speciation
Version: 1.0
Date: 2014-09-09
Depends: R (>= 2.14.2), geiger, caper, ape, deSolve, matrixStats
Author: Rampal S. Etienne & Alex L. Pigot
Maintainer: Rampal S. Etienne
License: GPL-2
Description: Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account the phylogenetic history
Packaged: 2014-09-09 18:19:08 UTC; p223208
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 09:29:22

More information about DAMOCLES at CRAN
Permanent link

Package RefManageR updated to version 0.8.40 with previous version 0.8.34 dated 2014-08-19

Title: Straightforward BibTeX and BibLaTeX Bibliography Management
Description: RefManageR provides tools for importing and working with bibliographic references. It greatly enhances the bibentry class by providing a class BibEntry which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. BibTeX and BibLaTeX .bib files can be read into R and converted to BibEntry objects. Interfaces to NCBI's Entrez, CrossRef, and Zotero are provided for importing references and references can be created from locally stored PDFs using Poppler. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with RMarkdown or RHTML.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean

Diff between RefManageR versions 0.8.34 dated 2014-08-19 and 0.8.40 dated 2014-10-29

 DESCRIPTION                   |    8 -
 MD5                           |  110 ++++++++---------
 NAMESPACE                     |    2 
 R/04InternalFunctions.R       |  260 +++++++++++++++++++++++++-----------------
 R/05makeBibLatex.R            |    4 
 R/07makeBibLatexAuthoryear.R  |    4 
 R/08asBibEntry.R              |   34 ++---
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 man/UpdateFieldName.Rd        |   13 --
 man/WriteBib.Rd               |   37 ++---
 man/as.BibEntry.Rd            |   18 +-
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 man/format_author.Rd          |    4 
 man/head.BibEntry.Rd          |   30 +---
 man/levels.BibEntry.Rd        |   16 +-
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 man/names.BibEntry.Rd         |   12 -
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 man/toRd.BibEntry.Rd          |   20 +--
 man/unlist.BibEntry.Rd        |   27 +---
 56 files changed, 1149 insertions(+), 1319 deletions(-)

More information about RefManageR at CRAN
Permanent link

New package rqPen with initial version 1.0
Package: rqPen
Type: Package
Title: R Package for Penalized Quantile Regression
Version: 1.0
Date: 2014-10-25
Author: Ben Sherwood
Depends: R (>= 3.0.0),quantreg
Maintainer: Ben Sherwood
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
ByteCompile: TRUE
License: MIT + file LICENSE
Packaged: 2014-10-29 01:29:00 UTC; bsherwoo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 07:44:31

More information about rqPen at CRAN
Permanent link

Package mlr updated to version 2.2 with previous version 2.1 dated 2014-07-21

Title: Machine Learning in R.
Description: Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Generic resampling, including cross-validation, bootstrapping and subsampling. Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems. Filter and wrapper methods for feature selection. Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre], Michel Lang [aut], Jakob Richter [aut], Jakob Bossek [aut], Leonard Judt [aut], Tobias Kuehn [aut], Erich Studerus [aut], Lars Kotthoff [aut]
Maintainer: Bernd Bischl

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More information about mlr at CRAN
Permanent link

Package deSolve updated to version 1.11 with previous version 1.10-9 dated 2014-06-25

Title: General Solvers for Initial Value Problems of Ordinary Differential Equations (ODE), Partial Differential Equations (PDE), Differential Algebraic Equations (DAE), and Delay Differential Equations (DDE)
Description: Functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations (PDE) that have been converted to ODEs by numerical differencing.
Author: Karline Soetaert [aut], Thomas Petzoldt [aut, cre], R. Woodrow Setzer [aut], odepack authors [cph]
Maintainer: Thomas Petzoldt

Diff between deSolve versions 1.10-9 dated 2014-06-25 and 1.11 dated 2014-10-29

 DESCRIPTION                    |    8 
 MD5                            |   84 +--
 NEWS                           |    7 
 R/DLLfunc.R                    |   79 ++-
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 R/functions.R                  |   13 
 R/iteration.R                  |   12 
 R/lsoda.R                      |   28 +
 R/lsodar.R                     |   36 +
 R/lsode.R                      |   34 +
 R/lsodes.R                     |  805 ++++++++++++++++---------------
 R/radau.R                      |   33 +
 R/rk.R                         |   22 
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 build/vignette.rds             |binary
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 inst/doc/compiledCode.R        |   23 
 inst/doc/compiledCode.Rnw      |  198 +++++++
 inst/doc/compiledCode.pdf      |binary
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 inst/doc/dynload/radaudaedll.R |    2 
 man/deSolve.Rd                 |    4 
 man/lsodes.Rd                  | 1048 ++++++++++++++++++++---------------------
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 src/errmsg.f                   |    8 
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 43 files changed, 1867 insertions(+), 1086 deletions(-)

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New package addreg with initial version 1.2
Package: addreg
Title: Additive Regression for Discrete Data
Description: Methods for fitting identity-link GLMs and GAMs to discrete data. The package uses EM-type algorithms with more stable convergence properties than standard methods.
Version: 1.2
Date: 2014-10-29
Author: Mark Donoghoe
Maintainer: Mark Donoghoe
Depends: R (>= 3.0.1)
Imports: splines, combinat, glm2
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-28 22:19:48 UTC; 42674999
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-29 07:36:11

More information about addreg at CRAN
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Tue, 28 Oct 2014

Package TSclust updated to version 1.2.2 with previous version 1.2.1 dated 2014-04-30

Title: Time series clustering utilities
Description: This package contains a set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.
Author: Pablo Montero Manso, José Antonio Vilar
Maintainer: Pablo Montero

Diff between TSclust versions 1.2.1 dated 2014-04-30 and 1.2.2 dated 2014-10-28

 ChangeLog       |    2 ++
 DESCRIPTION     |    6 +++---
 MD5             |   10 +++++-----
 R/diss.R        |    6 +++---
 man/diss.PDC.Rd |    6 +++---
 man/diss.Rd     |    4 ++--
 6 files changed, 18 insertions(+), 16 deletions(-)

More information about TSclust at CRAN
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Package robustreg updated to version 0.1-7 with previous version 0.1-5 dated 2014-10-09

Title: Robust Regression Functions
Description: Linear regression functions using Huber and Bisquare psi functions
Author: Ian M. Johnson
Maintainer: Ian M. Johnson

Diff between robustreg versions 0.1-5 dated 2014-10-09 and 0.1-7 dated 2014-10-28

 DESCRIPTION        |   15 ++--
 MD5                |   17 +++-
 NAMESPACE          |    8 +-
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 10 files changed, 210 insertions(+), 199 deletions(-)

More information about robustreg at CRAN
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Package logconPH updated to version 1.3 with previous version 1.2 dated 2014-10-25

Title: CoxPH Model with Log Concave Baseline Distribution
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman

Diff between logconPH versions 1.2 dated 2014-10-25 and 1.3 dated 2014-10-28

 DESCRIPTION                  |    8 ++++----
 MD5                          |    6 +++---
 src/Cpp2Source/baseClass.cpp |   20 +++++++-------------
 src/Cpp2Source/baseClass.h   |   15 +--------------
 4 files changed, 15 insertions(+), 34 deletions(-)

More information about logconPH at CRAN
Permanent link

New package MfUSampler with initial version 0.9
Package: MfUSampler
Type: Package
Title: Multivariate-from-Univariate (MfU) MCMC Sampler
Version: 0.9
Date: 2014-10-27
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Convenience Functions for Multivariate MCMC Using Univariate Samplers, including Slice Sampler with Stepout and Shrinkage (Neal, 2003), and Adaptive Rejection Sampler (Gilks and Wild, 1992).
License: GPL (>= 2)
Depends: ars
Suggests: sns
Packaged: 2014-10-28 18:54:28 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 22:00:52

More information about MfUSampler at CRAN
Permanent link

Package FAOSTAT updated to version 1.9 with previous version 1.6 dated 2014-03-14

Title: A complementary package to the FAOSTAT database and the Statistical Yearbook of the Food and Agricultural Organization of the United Nations.
Description: The package hosts a list of functions to automatically download statistics from FAOSTAT (database of the Food and Agricultural Organization of the United Nations) and WDI (database of the World Bank), and to perform some harmonization operations.
Author: Michael C. J. Kao , Markus Gesmann, Filippo Gheri
Maintainer: Filippo Gheri

Diff between FAOSTAT versions 1.6 dated 2014-03-14 and 1.9 dated 2014-10-28

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 FAOSTAT-1.9/FAOSTAT/R/FAOcheck.R                 |   94 ++++++++---
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 FAOSTAT-1.9/FAOSTAT/R/chConstruct.R              |   66 +++----
 FAOSTAT-1.9/FAOSTAT/R/chgr.R                     |   90 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/constructSYB.R             |  192 +++++++++++------------
 FAOSTAT-1.9/FAOSTAT/R/fillCountryCode.R          |   68 ++++----
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 FAOSTAT-1.9/FAOSTAT/R/getWDImetaData.R           |  150 ++++++++---------
 FAOSTAT-1.9/FAOSTAT/R/getWDItoSYB.R              |    2 
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 FAOSTAT-1.9/FAOSTAT/R/indConstruct.R             |   84 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/lsgr.R                     |  148 ++++++++---------
 FAOSTAT-1.9/FAOSTAT/R/mergeSYB.R                 |   84 +++++-----
 FAOSTAT-1.9/FAOSTAT/R/overlap.R                  |   37 +++-
 FAOSTAT-1.9/FAOSTAT/R/printLab.R                 |   58 +++---
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 FAOSTAT-1.9/FAOSTAT/demo/00Index                 |    2 
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 FAOSTAT-1.9/FAOSTAT/man/FAOmetaTable.Rd          |   22 +-
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 FAOSTAT-1.9/FAOSTAT/man/FAOsearch.Rd             |   25 +-
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 FAOSTAT-1.9/FAOSTAT/man/ebind.Rd                 |   44 ++---
 FAOSTAT-1.9/FAOSTAT/man/fillCountryCode.Rd       |   40 ++--
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 FAOSTAT-1.9/FAOSTAT/man/getFAO.Rd                |  112 ++++++-------
 FAOSTAT-1.9/FAOSTAT/man/getFAOtoSYB.Rd           |  116 ++++++-------
 FAOSTAT-1.9/FAOSTAT/man/getWDI.Rd                |   86 +++++-----
 FAOSTAT-1.9/FAOSTAT/man/getWDImetaData.Rd        |   55 +++---
 FAOSTAT-1.9/FAOSTAT/man/getWDItoSYB.Rd           |  106 ++++++------
 FAOSTAT-1.9/FAOSTAT/man/grConstruct.Rd           |   76 ++++-----
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 77 files changed, 1964 insertions(+), 1844 deletions(-)

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Permanent link

New package CateSelection with initial version 1.0
Package: CateSelection
Type: Package
Title: Categorical Variable Selection Methods
Version: 1.0
Date: 2014-10-28
Author: Yi Xu and Jixiang Wu
Maintainer: Yi Xu
Description: A multi-factor dimensionality reduction based forward selection method for genetic association mapping.
License: GPL (>= 2)
Depends: R(>= 2.10)
Repository: CRAN
Packaged: 2014-10-28 20:38:02 UTC; Xu
NeedsCompilation: no
Date/Publication: 2014-10-28 21:58:29

More information about CateSelection at CRAN
Permanent link

Package rgl updated to version 0.95.1157 with previous version 0.94.1143 dated 2014-09-30

Title: 3D visualization device system (OpenGL)
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler , Duncan Murdoch , and others (see README)
Maintainer: Duncan Murdoch

Diff between rgl versions 0.94.1143 dated 2014-09-30 and 0.95.1157 dated 2014-10-28

 rgl-0.94.1143/rgl/src/QuadSet.cpp         |only
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 rgl-0.95.1157/rgl/R/obj.R                 |  618 ++++++++++++++--------------
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 rgl-0.95.1157/rgl/R/turn3d.R              |  122 ++---
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 rgl-0.95.1157/rgl/src/NULLgui.cpp         |    2 
 rgl-0.95.1157/rgl/src/RenderContext.h     |    2 
 rgl-0.95.1157/rgl/src/Texture.cpp         |  225 +++++-----
 rgl-0.95.1157/rgl/src/Viewpoint.cpp       |   10 
 rgl-0.95.1157/rgl/src/device.cpp          |    3 
 rgl-0.95.1157/rgl/src/rglview.cpp         |   19 
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 59 files changed, 2883 insertions(+), 2849 deletions(-)

More information about rgl at CRAN
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Package knitcitations updated to version 1.0.4 with previous version 1.0-1 dated 2014-07-12

Title: Citations for knitr markdown files
Description: knitcitations provides the ability to create dynamic citations in which the bibliographic information is pulled from the web rather than having to be entered into a local database such as bibtex ahead of time. Knitcitations is primarily aimed at authoring in the R markdown format, and can provide outputs for web-based authoring such as linked text and tooltips over inline citations. Cite using a DOI, URL, or bibtex file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger

Diff between knitcitations versions 1.0-1 dated 2014-07-12 and 1.0.4 dated 2014-10-28

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More information about knitcitations at CRAN
Permanent link

New package safi with initial version 1.0
Package: safi
Type: Package
Title: Sensitivity Analysis for Functional Input
Version: 1.0
Date: 2014-10-28
Author: Jana Fruth, Malte Jastrow
Maintainer: Jana Fruth
Description: Design and sensitivity analysis for computer experiments with scalar-valued output and functional input, e.g. over time or space. The aim is to explore the behavior of the sensitivity over the functional domain.
License: GPL (>= 2)
Packaged: 2014-10-28 15:53:50 UTC; Jana
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 17:35:33

More information about safi at CRAN
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Package hht updated to version 2.1.1 with previous version 2.1.0 dated 2014-09-23

Title: The Hilbert-Huang Transform: Tools and Methods
Description: This package builds on the EMD package to provide additional tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also implements the ensemble empirical decomposition (EEMD) and the complete ensemble empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency problems found in EMD analysis. The package comes with several plotting methods that can be used to view intrinsic mode functions, the HHT spectrum, and the Fourier spectrum. To see the version history and download the bleeding-edge version (at your own risk!), see the project website at code.google.com below. See the other links for PDF files describing numerical and exact analytical methods for determining instantaneous frequency, some examples of signals processed with this package, and some examples of the ensemble empirical mode decomposition method.
Author: Daniel C. Bowman [aut, cre], Jonathan M. Lees [ctb]
Maintainer: Daniel C. Bowman

Diff between hht versions 2.1.0 dated 2014-09-23 and 2.1.1 dated 2014-10-28

 DESCRIPTION                      |   10 ++---
 MD5                              |   16 ++++----
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 9 files changed, 102 insertions(+), 45 deletions(-)

More information about hht at CRAN
Permanent link

Package timeSeries updated to version 3011.98 with previous version 3010.97 dated 2013-05-01

Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz

Diff between timeSeries versions 3010.97 dated 2013-05-01 and 3011.98 dated 2014-10-28

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Package etasFLP updated to version 1.1.0 with previous version 1.0.3 dated 2014-04-14

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

Diff between etasFLP versions 1.0.3 dated 2014-04-14 and 1.1.0 dated 2014-10-28

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More information about etasFLP at CRAN
Permanent link

Package BSSasymp updated to version 1.1-0 with previous version 1.0-2 dated 2014-08-07

Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates.
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen

Diff between BSSasymp versions 1.0-2 dated 2014-08-07 and 1.1-0 dated 2014-10-28

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New package settings with initial version 0.1.1
Package: settings
Type: Package
Title: Software Option Settings Manager for R
Version: 0.1.1
Date: 2014-10-22
Author: Mark van der Loo
Maintainer: Mark van der Loo
Description: Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names and default values. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes.
URL: https://github.com/markvanderloo/settings
License: GPL-3
VignetteBuilder: knitr
Suggests: testthat, knitr
Packaged: 2014-10-28 07:43:29 UTC; mark
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-28 11:18:40

More information about settings at CRAN
Permanent link

Package pander updated to version 0.5.0 with previous version 0.3.8 dated 2013-09-12

Title: An R pandoc writer
Description: Contains some functions catching all messages, stdout and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in Pandoc's markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex Pandoc documents to e.g. HTML, pdf, docx or odt. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching backend.
Author: Gergely Daróczi , Roman Tsegelskyi
Maintainer: Gergely Daróczi

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Package TR8 updated to version 0.9 with previous version 0.8 dated 2014-08-26

Title: A tool for downloading functional traits data for plant species
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.
Author: Gionata Bocci
Maintainer: Gionata Bocci

Diff between TR8 versions 0.8 dated 2014-08-26 and 0.9 dated 2014-10-28

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More information about TR8 at CRAN
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Package seqMeta updated to version 1.5 with previous version 1.4 dated 2014-04-10

Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Arie Voorman

Diff between seqMeta versions 1.4 dated 2014-04-10 and 1.5 dated 2014-10-28

 DESCRIPTION             |   13 +-
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More information about seqMeta at CRAN
Permanent link

Package qmethod updated to version 1.2.2 with previous version 1.2 dated 2014-10-24

Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology data to identify the distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org). The function qmethod() runs the full analysis. Each step can be run separately using the corresponding functions: qflag() for automatic flagging of Q-sorts (manual flagging is optional), qzscores() for scores for statements, qda() for distinguishing and consensus statements, and qfcharact() for general characteristics of the factors. Additional functions import data from PQMethod software, export plain text data for interpretation in two flavours, print and plot Q method results in a synthetic manner. The package uses principal components and it offers the following choices: manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
Author: Aiora Zabala [aut, cre]
Maintainer: Aiora Zabala

Diff between qmethod versions 1.2 dated 2014-10-24 and 1.2.2 dated 2014-10-28

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More information about qmethod at CRAN
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Package lassoscore updated to version 0.6 with previous version 0.5 dated 2014-05-09

Title: High-Dimensional Inference with the Penalized Score Test
Description: Use the lasso regression method to perform approximate inference in high dimensions, by penalizing the effects of nuisance parameters.
Author: Arie Voorman
Maintainer: Arie Voorman

Diff between lassoscore versions 0.5 dated 2014-05-09 and 0.6 dated 2014-10-28

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More information about lassoscore at CRAN
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Package energy updated to version 1.6.2 with previous version 1.6.1 dated 2014-02-23

Title: E-statistics (energy statistics)
Description: E-statistics (energy) tests and statistics for comparing distributions: multivariate normality, multivariate distance components and k-sample test for equal distributions, hierarchical clustering by e-distances, multivariate independence tests, distance correlation, goodness-of-fit tests. Energy- statistics concept based on a generalization of Newton's potential energy is due to Gabor J. Szekely.
Author: Maria L. Rizzo and Gabor J. Szekely
Maintainer: Maria Rizzo

Diff between energy versions 1.6.1 dated 2014-02-23 and 1.6.2 dated 2014-10-28

 DESCRIPTION  |    8 ++++----
 MD5          |    8 ++++----
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More information about energy at CRAN
Permanent link

Package Ecfun updated to version 0.1-2 with previous version 0.1-0 dated 2014-04-08

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves

Diff between Ecfun versions 0.1-0 dated 2014-04-08 and 0.1-2 dated 2014-10-28

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Package HPO.db (with last version 1.2) was removed from CRAN

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

2013-07-04 1.2
2012-10-30 1.0

Permanent link
Package HPOSim (with last version 1.2) was removed from CRAN

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

2014-02-21 1.2
2013-07-05 1.1
2013-03-28 1.0

Permanent link

Mon, 27 Oct 2014

Package timeDate updated to version 3011.99 with previous version 3010.98 dated 2013-05-01

Title: Rmetrics - Chronological and Calendar Objects
Description: Environment for teaching "Financial Engineering and Computational Finance".
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb], Martin Maechler [ctb], Joe W. Byers [ctb]
Maintainer: Tobias Setz

Diff between timeDate versions 3010.98 dated 2013-05-01 and 3011.99 dated 2014-10-27

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Package sirt updated to version 1.0-3 with previous version 0.47-36 dated 2014-08-30

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch

Diff between sirt versions 0.47-36 dated 2014-08-30 and 1.0-3 dated 2014-10-27

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Package RQDA updated to version 0.2-7 with previous version 0.2-6 dated 2014-05-11

Title: R-based Qualitative Data Analysis
Description: R package for Qualitative Data Analysis. Current version only supports plain text, but it can import PDF highlights if the Enhance package of rjpod, which is available on R-Forge, is installed.
Author: HUANG Ronggui
Maintainer: HUANG Ronggui

Diff between RQDA versions 0.2-6 dated 2014-05-11 and 0.2-7 dated 2014-10-27

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More information about RQDA at CRAN
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Package rjags updated to version 3-14 with previous version 3-13 dated 2014-03-06

Title: Bayesian graphical models using MCMC
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb]
Maintainer: Martyn Plummer

Diff between rjags versions 3-13 dated 2014-03-06 and 3-14 dated 2014-10-27

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Package rangeMapper updated to version 0.2-8 with previous version 0.2-6 dated 2014-02-07

Title: A platform for the study of macroecology of life history traits
Description: Tools for easy generation of (life-history) traits maps based on species range (extent-of-occurrence) maps.
Author: Mihai Valcu , James Dale
Maintainer: Mihai Valcu

Diff between rangeMapper versions 0.2-6 dated 2014-02-07 and 0.2-8 dated 2014-10-27

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More information about rangeMapper at CRAN
Permanent link

New package bio3d with initial version 2.1-3
Package: bio3d
Title: Biological Structure Analysis
Version: 2.1-3
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
VignetteBuilder: knitr
Imports: parallel, grid
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1)
Depends: R (>= 3.1.0)
LazyData: yes
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintainer: Barry Grant
License: GPL (>= 2)
URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d
Packaged: 2014-10-24 21:47:52 UTC; xinqyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-27 19:03:11

More information about bio3d at CRAN
Permanent link

New package h2o with initial version 2.8.1.1
Package: h2o
Type: Package
Title: H2O R Interface
Version: 2.8.1.1
Date: 2014-05-15
Author: Anqi Fu, Spencer Aiello, Ariel Rao, Tom Kraljevic and Petr Maj, with contributions from the 0xdata team
Maintainer: Tom Kraljevic
Description: Run H2O via its REST API from within R.
License: Apache License (== 2.0)
Depends: R (>= 2.13.0), RCurl, rjson, statmod, survival, stats, tools, utils, methods
Collate: Wrapper.R Internal.R Classes.R ParseImport.R models.R Algorithms.R zzz.R
NeedsCompilation: no
SystemRequirements: Java (>= 1.6)
Suggests: plyr
URL: http://www.0xdata.com
Packaged: 2014-10-23 02:24:40 UTC; jenkins
Repository: CRAN
Date/Publication: 2014-10-27 18:11:24

More information about h2o at CRAN
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Package DALY updated to version 1.4.0 with previous version 1.3.0 dated 2014-05-10

Title: DALY Calculator - A GUI for stochastic DALY calculation in R
Description: The DALY Calculator is a free, open-source Graphical User Interface (GUI) for stochastic disability-adjusted life year (DALY) calculation.
Author: Brecht Devleesschauwer [aut, cre], Scott McDonald [aut], Juanita Haagsma [aut], Nicolas Praet [aut], Arie Havelaar [aut], Niko Speybroeck [aut]
Maintainer: Brecht Devleesschauwer

Diff between DALY versions 1.3.0 dated 2014-05-10 and 1.4.0 dated 2014-10-27

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Permanent link

Package bdscale updated to version 1.1 with previous version 1.0 dated 2014-10-08

Title: Remove Weekends and Holidays From ggplot2 Axes
Description: Provides a continuous date scale, omitting weekends and holidays.
Author: Dave Mills
Maintainer: Dave Mills

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Package RGA updated to version 0.1.3 with previous version 0.1.2 dated 2014-09-01

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.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov

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New package qdm with initial version 0.1-0
Package: qdm
Version: 0.1-0
Date: 2014-10-16
Title: Fitting a Quadrilateral Dissimilarity Model to Same-Different Judgments
Authors@R: c(person("Nora", "Umbach", role = c("aut", "cre"), email = "nora.umbach@web.de"), person("Florian", "Wickelmaier", role = "aut"))
Depends: R (>= 3.1.0), stats, graphics
Description: This package provides different specifications of a Quadrilateral Dissimilarity Model which can be used to fit same-different judgments in order to get a predicted matrix that satisfies regular minimality [Colonius & Dzhafarov, 2006, Measurement and representations of sensations, Erlbaum]. From such a matrix, Fechnerian distances can be computed.
License: GPL (>= 2)
Packaged: 2014-10-27 13:33:02 UTC; noraumbach
Author: Nora Umbach [aut, cre], Florian Wickelmaier [aut]
Maintainer: Nora Umbach
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-27 15:30:23

More information about qdm at CRAN
Permanent link

Package fICA updated to version 1.0-2 with previous version 1.0-1 dated 2014-09-05

Title: Classical, Reloaded and Adaptive FastICA Algorithms
Description: Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen

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Package choroplethr updated to version 2.0.0 with previous version 1.7.0 dated 2014-06-14

Title: Simplify the creation of choropleth maps in R.
Description: choroplethr simplifies the creation of choropleth maps in R. Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. choroplethr simplifies this process by 1. Providing ready-made functions for creating choropleths using four different maps. 2. Providing API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein [cre, aut], Brian P Johnson [ctb, frontend animation code]
Maintainer: Ari Lamstein

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Package astsa updated to version 1.3 with previous version 1.2 dated 2014-03-17

Title: Applied Statistical Time Series Analysis
Description: Data sets and scripts for Time Series Analysis and Its Applications: With R Examples by Shumway and Stoffer, 3rd edition
Author: David Stoffer
Maintainer: David Stoffer

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Package sqldf updated to version 0.4-9 with previous version 0.4-7.1 dated 2014-03-15

Title: Perform SQL Selects on R Data Frames
Description: Description: Manipulate R data frames using SQL.
Author: G. Grothendieck
Maintainer: G. Grothendieck

Diff between sqldf versions 0.4-7.1 dated 2014-03-15 and 0.4-9 dated 2014-10-27

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Package ropensecretsapi updated to version 1.0.1 with previous version 1.0.0 dated 2014-10-05

Title: R Package for the OpenSecrets.org API
Description: An R package for the OpenSecrets.org web services API.
Author: Thomas P. Fuller
Maintainer: Thomas P. Fuller

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Package PopGenReport updated to version 2.1 with previous version 2.0 dated 2014-07-04

Title: PopGenReport: A simple way to analyse and visualize population genetic data
Description: This package provides an easy way to analyse population genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber

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Package pitchRx updated to version 1.6 with previous version 1.5 dated 2014-07-23

Title: Tools for Harnessing MLBAM Gameday data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced Media's Gameday data (as well as store it in a remote database). The Gameday website hosts a wealth of data in XML format, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball's flight path from a pitcher's hand to home plate. With pitchRx, one can easily create animations and interactive 3D scatterplots of the baseball's flight path. PITCHf/x data is also commonly used to generate a static plot of baseball locations at the moment they cross home plate. These plots, sometimes called strike-zone plots, can also refer to a plot of event probabilities over the same region. pitchRx provides an easy and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert
Maintainer: Carson Sievert

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Sun, 26 Oct 2014

Package RSelenium updated to version 1.3.5 with previous version 1.3.1 dated 2014-05-25

Title: R bindings for Selenium WebDriver.
Description: The RSelenium package provides a set of R bindings for the Selenium 2.0 WebDriver using the JsonWireProtocol. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.
Author: John Harrison
Maintainer: John Harrison

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Package statar updated to version 0.1.1 with previous version 0.1 dated 2014-10-16

Title: Tools Inspired by Stata to Clean, Explore and Join Datasets
Description: statar makes it easier to work with tabular datasets. statar includes a set of functions to clean and summarize variables, to join datasets with an SQL-syntax, and to manipulate datasets with a panel structure (elapsed dates, lead/lag, fill rows for missing dates, fill in missing values). statar is based on the data.table package and is inspired by Stata.
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez

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Package rdrobust updated to version 0.70 with previous version 0.61 dated 2014-09-04

Title: Robust data-driven statistical inference in Regression-Discontinuity designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect to perform bandwidth selection for the different procedures implemented, and rdplot to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico , Matias D. Cattaneo , Rocio Titiunik
Maintainer: Sebastian Calonico

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