Thu, 11 Feb 2016

Package timedelay updated to version 1.0.2 with previous version 1.0.1 dated 2016-01-05

Title: Time Delay Estimation for Stochastic Time Series of Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>

Diff between timedelay versions 1.0.1 dated 2016-01-05 and 1.0.2 dated 2016-02-11

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Package RPPanalyzer updated to version 1.4.3 with previous version 1.4.1 dated 2015-06-24

Title: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data
Description: Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.
Author: Heiko Mannsperger with contributions of Stephan Gade
Maintainer: Astrid Wachter <astrid.wachter@med.uni-goettingen.de>

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Package emdbook updated to version 1.3.9 with previous version 1.3.8 dated 2015-05-01

Title: Support Functions and Data for "Ecological Models and Data"
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker
Maintainer: Ben Bolker <bolker@mcmaster.ca>

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Package BSSasymp updated to version 1.1-2 with previous version 1.1-1 dated 2015-08-17

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 and squared 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 <jari.p.miettinen@jyu.fi>

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Package BGPhazard updated to version 1.2.3 with previous version 1.2.2 dated 2015-03-17

Title: Markov Beta and Gamma Processes for Modeling Hazard Rates
Description: Computes the hazard rate estimate as described by Nieto-Barajas and Walker (2002) and Nieto-Barajas (2003).
Author: L. E. Nieto-Barajas and J. A. Garcia Bueno
Maintainer: Jose Antonio Garcia Bueno <joseagbueno@gmail.com>

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Package bbmle updated to version 1.0.18 with previous version 1.0.17 dated 2014-05-27

Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.
Author: Ben Bolker <bolker@mcmaster.ca>, R Development Core Team
Maintainer: Ben Bolker <bolker@mcmaster.ca>

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Package AICcmodavg updated to version 2.0-4 with previous version 2.0-3 dated 2015-01-16

Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>.
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>

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New package MDplot with initial version 0.2
Package: MDplot
Version: 0.2
Date: 2016-02-09
Authors@R: person( given = "Christian", family = "Margreitter", email = "christian.margreitter@gmail.com", role = c( "aut", "cre" ) )
Title: Visualizing Molecular Dynamics Analysis
Depends: R (>= 3.0.0), methods, MASS, RColorBrewer, gplots, gtools
Description: Provides automatization for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis.
License: GPL-3
LazyLoad: yes
Author: Christian Margreitter [aut, cre]
Maintainer: Christian Margreitter <christian.margreitter@gmail.com>
NeedsCompilation: no
Repository: CRAN
Packaged: 2016-02-11 13:08:27 UTC; margreitterc
Date/Publication: 2016-02-11 14:28:36

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Package svd updated to version 0.4 with previous version 0.3.3-2 dated 2014-03-07

Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>

Diff between svd versions 0.3.3-2 dated 2014-03-07 and 0.4 dated 2016-02-11

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New package tweenr with initial version 0.1.2
Package: tweenr
Type: Package
Title: Interpolate Data for Smooth Animations
Version: 0.1.2
Date: 2016-02-11
Authors@R: c( person('Thomas Lin', 'Pedersen', , 'thomasp85@gmail.com', c('aut', 'cre')) )
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Description: In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that plugs right into functions such as gg_animate() from the 'gganimate' package. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and colour.
URL: https://github.com/thomasp85/tweenr
BugReports: https://github.com/thomasp85/tweenr/issues
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.12.3), grDevices
LinkingTo: Rcpp
Collate: 'RcppExports.R' 'aaa.R' 'tween_numeric.R' 'display_ease.R' 'interpolate.R' 'tween_colour.R' 'tween_datetime.R' 'tween_date.R' 'tween.R' 'tween_appear.R' 'tween_constant.R' 'tween_elements.R' 'tween_states.R' 'tweenr_package.R'
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-02-11 10:36:27 UTC; Thomas
Author: Thomas Lin Pedersen [aut, cre]
Repository: CRAN
Date/Publication: 2016-02-11 12:23:39

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Package starma updated to version 1.3 with previous version 1.2 dated 2015-11-12

Title: Modelling Space Time AutoRegressive Moving Average (STARMA) Processes
Description: Statistical functions to identify, estimate and diagnose a Space-Time AutoRegressive Moving Average (STARMA) model.
Author: Felix Cheysson
Maintainer: Felix Cheysson <felix@cheysson.fr>

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Package sjmisc updated to version 1.5 with previous version 1.4 dated 2016-01-13

Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/ or who are new to R), supporting following common tasks: 1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc. 2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. 3) Convenient functions to perform frequently used statistical tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package seasonal updated to version 1.2.1 with previous version 1.2.0 dated 2016-01-28

Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the seasonal adjustment software by the US Census Bureau. It offers full access to almost all options and outputs of X-13, including X-11 and SEATS, automatic ARIMA model search, outlier detection and support for user defined holiday variables, such as Chinese New Year or Indian Diwali. It also includes a Shiny-based graphical user interface. Seasonal uses the X-13 binaries from the 'x13binary' package.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>

Diff between seasonal versions 1.2.0 dated 2016-01-28 and 1.2.1 dated 2016-02-11

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Package npregfast updated to version 1.2.0 with previous version 1.0.1 dated 2015-11-16

Title: Nonparametric Estimation of Regression Models with Factor-by-Curve Interactions
Description: A method for obtain nonparametric estimates of regression models with or without factor-by-curve interactions using local polynomial kernel smoothers. Additionally, a parametric model (allometric model) can be estimated.
Author: Marta Sestelo [aut, cre], Nora M. Villanueva [aut], Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>

Diff between npregfast versions 1.0.1 dated 2015-11-16 and 1.2.0 dated 2016-02-11

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Package kintone (with last version 0.1.1) was removed from CRAN

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

2014-03-22 0.1.1
2014-03-09 0.1

Permanent link
Package Taxonstand updated to version 1.8 with previous version 1.7 dated 2014-12-15

Title: Taxonomic Standardization of Plant Species Names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using 'The Plant List' website (www.theplantlist.org).
Author: Luis Cayuela, Jari Oksanen
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>

Diff between Taxonstand versions 1.7 dated 2014-12-15 and 1.8 dated 2016-02-11

 DESCRIPTION  |    8 ++++----
 MD5          |   10 +++++-----
 NAMESPACE    |    1 +
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 6 files changed, 26 insertions(+), 20 deletions(-)

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Package VarfromPDB updated to version 2.0.5 with previous version 1.1.0 dated 2015-12-21

Title: Capture the Genes and Variants Related to a Genetic Disease from Public Databases
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, http://human-phenotype-ontology.github.io/about.html), Orphanet (http://www.orpha.net/consor/cgi-bin/index.php), OMIM (Online Mendelian Inheritance in Man, http://www.omim.org), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar), and Uniprot (Universal Protein Resource, http://www.uniprot.org) and Pubmed. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. Uniprot focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the Uniprot are manually curated from UniProtKB/Swiss-Prot.
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu@gmail.com>

Diff between VarfromPDB versions 1.1.0 dated 2015-12-21 and 2.0.5 dated 2016-02-11

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More information about VarfromPDB at CRAN
Permanent link

Package SpatPCA updated to version 1.1.1.0 with previous version 1.1.0.0 dated 2015-11-01

Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>

Diff between SpatPCA versions 1.1.0.0 dated 2015-11-01 and 1.1.1.0 dated 2016-02-11

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Permanent link

New package spacom with initial version 1.0-5
Package: spacom
Type: Package
Title: Spatially Weighted Context Data for Multilevel Modelling
Version: 1.0-5
Date: 2016-02-10
Authors@R: c(person("Till", "Junge", role = c("aut", "cre"), email = "till.junge@altermail.ch"), person("Sandra", "Penic", role = "aut", email = "sandra.penic@unil.ch"), person("Mathieu", "Cossuta", role = "aut", email = "mcossutta@gmail.com"), person("Guy", "Elcheroth", role = "aut", email = "guy.elcheroth@unil.ch"), person("Stephanie", "Glaeser", role = "ctb", email = "stephanie.glaeser@unil.ch"), person("Davide", "Morselli", role = "ctb", email = "davide.morselli@unil.ch"))
Description: Provides tools to construct and exploit spatially weighted context data. Spatial weights are derived by a Kernel function from a user-defined matrix of distances between contextual units. Spatial weights can then be applied either to precise contextual measures or to aggregate estimates based on micro-level survey data, to compute spatially weighted context data. Available aggregation functions include indicators of central tendency, dispersion, or inter-group variability, and take into account survey design weights. The package further allows combining the resulting spatially weighted context data with individual-level predictor and outcome variables, for the purposes of multilevel modelling. An ad hoc stratified bootstrap resampling procedure generates robust point estimates for multilevel regression coefficients and model fit indicators, and computes confidence intervals adjusted for measurement dependency and measurement error of aggregate estimates. As an additional feature, residual and explained spatial dependency can be estimated for the tested models.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.3.2)
Imports: methods, spdep, foreach, iterators, lme4, nlme, Matrix
Collate: all_classes.R common.R moran.R SpawML.R Descriptives.R ResExSpawML.R ResAggSpawML.R Weights.R ExplorSpawML.R
NeedsCompilation: no
Packaged: 2016-02-11 00:53:01 UTC; junge
Author: Till Junge [aut, cre], Sandra Penic [aut], Mathieu Cossuta [aut], Guy Elcheroth [aut], Stephanie Glaeser [ctb], Davide Morselli [ctb]
Maintainer: Till Junge <till.junge@altermail.ch>
Repository: CRAN
Date/Publication: 2016-02-11 08:27:52

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New package serial with initial version 1.1
Package: serial
Type: Package
Title: The Serial Interface Package
Version: 1.1
Date: 2016-02-04
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>
Description: Provides functionality for the use of the internal hardware RS232/RS422/RS485 or any other virtual serial interfaces of the computer.
Depends: R (>= 2.15.0)
License: GPL-2
RoxygenNote: 5.0.1
Packaged: 2016-02-11 06:37:12 UTC; ms5760
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-02-11 08:52:54

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Package rcbalance updated to version 1.8.2 with previous version 1.8.0 dated 2015-12-14

Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>

Diff between rcbalance versions 1.8.0 dated 2015-12-14 and 1.8.2 dated 2016-02-11

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 8 files changed, 38 insertions(+), 23 deletions(-)

More information about rcbalance at CRAN
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Package MCMCpack updated to version 1.3-4 with previous version 1.3-3 dated 2013-05-01

Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return coda mcmc objects that can then be summarized using the coda package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>

Diff between MCMCpack versions 1.3-3 dated 2013-05-01 and 1.3-4 dated 2016-02-11

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Package EnsembleBase updated to version 1.0.1 with previous version 1.0.0 dated 2016-01-18

Title: Extensible Package for Parallel, Batch Training of Base Learners for Ensemble Modeling
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, K-Nearest Neighbors, Penalized Regression (L1/L2), and Bayesian Additive Regression Trees. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>

Diff between EnsembleBase versions 1.0.0 dated 2016-01-18 and 1.0.1 dated 2016-02-11

 ChangeLog             |   25 ++++++++++++++-----------
 DESCRIPTION           |    8 ++++----
 MD5                   |   18 +++++++++---------
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 10 files changed, 34 insertions(+), 31 deletions(-)

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New package ARTP2 with initial version 0.9.21
Package: ARTP2
Type: Package
Title: Pathway and Gene-Level Association Test
Version: 0.9.21
Date: 2016-02-10
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang
Maintainer: Han Zhang <han.zhang2@nih.gov>
Depends: R (>= 2.10), parallel, Formula, data.table, stats, utils
Description: Pathway and gene level association test using raw data or summary statistics.
License: GPL-2 | GPL-3
URL: https://github.com/zhangh12/ARTP2
NeedsCompilation: yes
Packaged: 2016-02-11 03:44:55 UTC; zhangh12
Repository: CRAN
Date/Publication: 2016-02-11 08:27:33

More information about ARTP2 at CRAN
Permanent link

Wed, 10 Feb 2016

Package VNM updated to version 4.1 with previous version 4.0 dated 2015-02-09

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 midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang <Yarong.Yang@ndsu.edu>

Diff between VNM versions 4.0 dated 2015-02-09 and 4.1 dated 2016-02-10

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Permanent link

New package titrationCurves with initial version 0.1.0
Package: titrationCurves
Type: Package
Title: Acid/Base, Complexation, Redox, and Precipitation Titration Curves
Version: 0.1.0
Date: 2016-02-09
Authors@R: person("David","Harvey", email = "harvey@depauw.edu", role = c("aut", "cre"))
Maintainer: David Harvey <harvey@depauw.edu>
Description: A collection of functions to plot acid/base titration curves (pH vs. volume of titrant), complexation titration curves (pMetal vs. volume of EDTA), redox titration curves (potential vs.volume of titrant), and precipitation titration curves (either pAnalyte or pTitrant vs. volume of titrant). Options include the titration of mixtures, the ability to overlay two or more titration curves, and the ability to show equivalence points.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-02-10 20:42:24 UTC; davidharvey
Author: David Harvey [aut, cre]
Repository: CRAN
Date/Publication: 2016-02-11 00:49:16

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Package pxweb updated to version 0.6.0 with previous version 0.5.57 dated 2015-07-14

Title: R Interface to the PX-Web/PC-Axis API
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API is used by organizations such as Statistics Sweden and Statistics Finland to disseminate data. The R package can interact with all PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract metadata and extract and parse statistics to R data.frame format. PX-Web is a solution to disseminate PC-Axis data files in dynamic tables on the web. Since 2013 PX-Web contains an API to disseminate PC-Axis files.
Author: Mans Magnusson, Leo Lahti, Love Hansson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>

Diff between pxweb versions 0.5.57 dated 2015-07-14 and 0.6.0 dated 2016-02-10

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 58 files changed, 306 insertions(+), 134 deletions(-)

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Package monomvn updated to version 1.9-6 with previous version 1.9-5 dated 2014-05-21

Title: Estimation for Multivariate Normal and Student-t Data with Monotone Missingness
Description: Estimation of multivariate normal and student-t data of arbitrary dimension where the pattern of missing data is monotone. Through the use of parsimonious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard regressions fail, the package can handle a nearly arbitrary amount of missing data. The current version supports maximum likelihood inference and a full Bayesian approach employing scale-mixtures for Gibbs sampling. Monotone data augmentation extends this Bayesian approach to arbitrary missingness patterns. A fully functional standalone interface to the Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown), Horseshoe (from Carvalho, Polson, & Scott), and ridge regression with model selection via Reversible Jump, and student-t errors (from Geweke) is also provided.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>

Diff between monomvn versions 1.9-5 dated 2014-05-21 and 1.9-6 dated 2016-02-10

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New package ionr with initial version 0.3.0
Package: ionr
Type: Package
Title: Test for Indifference of Indicator
Version: 0.3.0
Date: 2016-10-02
Author: Uku Vainik <ukuvainik@gmail.com>, Rene Mottus <rene.mottus@ed.ac.uk>
Maintainer: Uku Vainik <ukuvainik@gmail.com>
Depends: R (>= 3.0)
Imports: gplots, psych
Suggests: lavaan
Description: Provides item exclusion procedure, which is a formal method to test 'Indifference Of iNdicator' (ION). When a latent personality trait-outcome association is assumed, then the association strength should not depend on which subset of indicators (i.e. items) has been chosen to reflect the trait. Personality traits are often measured (reflected) by a sum-score of a certain set of indicators. Item exclusion procedure randomly excludes items from a sum-score and tests, whether the sum-score - outcome correlation changes. ION has been achieved, when any item can be excluded from the sum-score without the sum-score - outcome correlation substantially changing . For more details, see Vainik, Mottus et. al, (2015) "Are Trait-Outcome Associations Caused by Scales or Particular Items? Example Analysis of Personality Facets and BMI",European Journal of Personality DOI: <10.1002/per.2009> .
License: GPL (>= 2)
NeedsCompilation: no
LazyData: TRUE
RoxygenNote: 5.0.1
Encoding: UTF-8
URL: www.ut.ee/uku.vainik/ion/
Packaged: 2016-02-10 20:16:09 UTC; uku
Repository: CRAN
Date/Publication: 2016-02-11 00:47:11

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Package x13binary updated to version 0.1.1 with previous version 0.1.0 dated 2016-01-19

Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census provides a seasonal adjustment program now called 'X-13ARIMA-SEATS' building on both earlier Census programs called X-11 and X-12 as well as the SEATS program by the Bank of Spain. Census offers both source and binary versions -- which this package integrates for use by other R packages.
Author: Dirk Eddelbuettel and Christoph Sax
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between x13binary versions 0.1.0 dated 2016-01-19 and 0.1.1 dated 2016-02-10

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Package TRADER updated to version 1.2-1 with previous version 1.2-0 dated 2015-11-20

Title: Tree Ring Analysis of Disturbance Events in R
Description: Tree Ring Analysis of Disturbance Events in R (TRADER) package provides only one way for disturbance reconstruction from tree-ring data.
Author: Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>

Diff between TRADER versions 1.2-0 dated 2015-11-20 and 1.2-1 dated 2016-02-10

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Package psData updated to version 0.2 with previous version 0.1.2 dated 2014-02-23

Title: Download Regularly Maintained Political Science Data Sets
Description: This R package includes functions for gathering commonly used and regularly maintained data set in political science. It also includes functions for combining components from these data sets into variables that have been suggested in the literature, but are not regularly maintained.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

Diff between psData versions 0.1.2 dated 2014-02-23 and 0.2 dated 2016-02-10

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Package pan updated to version 1.4 with previous version 1.3 dated 2015-02-10

Title: Multiple Imputation for Multivariate Panel or Clustered Data
Description: Multiple imputation for multivariate panel or clustered data.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

Diff between pan versions 1.3 dated 2015-02-10 and 1.4 dated 2016-02-10

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New package npmr with initial version 1.0
Package: npmr
Type: Package
Title: Nuclear Penalized Multinomial Regression
Version: 1.0
Date: 2016-02-09
Author: Scott Powers, Trevor Hastie, Robert Tibshirani
Maintainer: Scott Powers <sspowers@stanford.edu>
Description: Fit multinomial logistic regression with a penalty on the nuclear norm of the estimated regression coefficient matrix, using proximal gradient descent.
License: GPL-2
Packaged: 2016-02-10 11:28:12 UTC; sspowers
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-02-10 18:57:25

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New package mvnTest with initial version 1.1-0
Package: mvnTest
Version: 1.1-0
Authors@R: c(person("Natalya", "Pya", role = c("aut", "cre"), email = "nat.pya@gmail.com"), person("Vassilly", "Voinov", role = "aut", email = "voinovv@kimep.kz"), person("Rashid", "Makarov", role = "aut", email = "rashidm@kimep.kz"), person("Yevgeniy", "Voinov", role = "aut", email = "v.yevgeniy@yahoo.com"))
Author: Natalya Pya [aut, cre], Vassilly Voinov [aut], Rashid Makarov [aut], Yevgeniy Voinov [aut]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Title: Goodness of Fit Tests for Multivariate Normality
Date: 2016-01-25
Description: Routines for assessing multivariate normality. Implements three Wald's type chi-squared tests; non-parametric Anderson-Darling and Cramer-von Mises tests; Doornik-Hansen test, Royston test and Henze-Zirkler test.
Depends: R (>= 2.15.0), mvtnorm
Imports: methods, stats, graphics, MASS
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-02-10 08:54:01 UTC; natalya
Repository: CRAN
Date/Publication: 2016-02-10 18:57:23

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New package GetTDData with initial version 1.0
Package: GetTDData
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Version: 1.0
Authors@R: person("Marcelo", "Perlin", email = "marceloperlin@gmail.com", role = c("aut", "cre"))
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Depends: R (>= 3.2.3)
Imports: stringr,xlsx,utils,stats
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-02-10 10:34:54 UTC; Marcelo
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Repository: CRAN
Date/Publication: 2016-02-10 18:57:02

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Package gaston updated to version 1.4 with previous version 1.3.1 dated 2015-12-14

Title: Genetic Data Manipulation (Quality Control, GRM and LD Computations, PCA), Linear Mixed Models (AIREML Algorithm), Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>

Diff between gaston versions 1.3.1 dated 2015-12-14 and 1.4 dated 2016-02-10

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Package fractional updated to version 0.1.2 with previous version 0.1.1 dated 2016-02-08

Title: Vulgar Fractions in R
Description: The main function of this package allows numerical vector objects to be displayed with their values in vulgar fractional form. This is convenient if patterns can then be more easily detected. In some cases replacing the components of a numeric vector by a rational approximation can also be expected to remove some component of round-off error. The main functions form a re-implementation of the functions 'fractions' and 'rational' of the MASS package, but using a radically improved programming strategy.
Author: Bill Venables
Maintainer: Bill Venables <bill.venables@gmail.com>

Diff between fractional versions 0.1.1 dated 2016-02-08 and 0.1.2 dated 2016-02-10

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New package exploreR with initial version 0.1
Package: exploreR
Type: Package
Title: Tools for Quickly Exploring Data
Version: 0.1
Date: 2016-02-10
Authors@R: person("Michael", "Coates", email = "azhain@gmail.com", role = c("aut", "cre"))
Description: Simplifies some complicated and labor intensive processes involved in exploring and explaining data. Allows you to quickly and efficiently visualize the interaction between variables and simplifies the process of discovering covariation in your data. Also includes some convenience features designed to remove as much redundant typing as possible.
Depends: R (>= 3.2.3)
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: ggplot2, grDevices, stats
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-02-10 15:16:40 UTC; Michael
Author: Michael Coates [aut, cre]
Maintainer: Michael Coates <azhain@gmail.com>
Repository: CRAN
Date/Publication: 2016-02-10 18:57:17

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Package dendextend updated to version 1.1.8 with previous version 1.1.2 dated 2015-10-31

Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

Diff between dendextend versions 1.1.2 dated 2015-10-31 and 1.1.8 dated 2016-02-10

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More information about dendextend at CRAN
Permanent link

New package codingMatrices with initial version 0.1.1
Package: codingMatrices
Type: Package
Title: Alternative Coding Matrices for Factors in Linear Model Formulae
Version: 0.1.1
Author: Bill Venables
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Description: A collection of coding functions as alternatives to the standard functions in the stats package, which have names starting with 'contr.'. Their main advantage is that they provide a consistent method for defining marginal effects in multi-way factorial models. In a simple one-way ANOVA model the intercept term is always the simple average of the class means.
Depends: stats
Imports: Matrix, methods, fractional
Suggests: MASS
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-02-10 12:41:08 UTC; Bill
Repository: CRAN
Date/Publication: 2016-02-10 18:57:08

More information about codingMatrices at CRAN
Permanent link

Package blockseg updated to version 0.2 with previous version 0.1 dated 2016-01-15

Title: Two Dimensional Change-Points Detection
Description: Segments a matrix in blocks with constant values.
Author: Julien Chiquet [aut, cre], Vincent Brault [aut]
Maintainer: Julien Chiquet <julien.chiquet@gmail.com>

Diff between blockseg versions 0.1 dated 2016-01-15 and 0.2 dated 2016-02-10

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Package tikzDevice updated to version 0.10-1 with previous version 0.10 dated 2016-02-06

Title: R Graphics Output in LaTeX Format
Description: Provides a graphics output device for R that records plots in a LaTeX-friendly format. The device transforms plotting commands issued by R functions into LaTeX code blocks. When included in a LaTeX document, these blocks are interpreted with the help of 'TikZ'---a graphics package for TeX and friends written by Till Tantau. Using the 'tikzDevice', the text of R plots can contain LaTeX commands such as mathematical formula. The device also allows arbitrary LaTeX code to be inserted into the output stream.
Author: Charlie Sharpsteen [aut], Cameron Bracken [aut], Kirill Müller [ctb, cre], Yihui Xie [ctb]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

Diff between tikzDevice versions 0.10 dated 2016-02-06 and 0.10-1 dated 2016-02-10

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More information about tikzDevice at CRAN
Permanent link

New package solrium with initial version 0.3.0
Package: solrium
Title: General Purpose R Interface to 'Solr'
Description: Provides a set of functions for querying and parsing data from 'Solr' (<http://lucene.apache.org/solr>) 'endpoints' (local and remote), including search, 'faceting', 'highlighting', 'stats', and 'more like this'. In addition, some functionality is included for creating, deleting, and updating documents in a 'Solr' 'database'.
Version: 0.3.0
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")
License: MIT + file LICENSE
URL: https://github.com/ropensci/solrium
BugReports: http://www.github.com/ropensci/solrium/issues
VignetteBuilder: knitr
Imports: stats, utils, methods, dplyr, plyr, httr (>= 1.0.0), XML, jsonlite
Suggests: testthat, knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-02-09 20:28:53 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2016-02-10 09:11:27

More information about solrium at CRAN
Permanent link

Package reservoir updated to version 1.1.4 with previous version 1.1.3 dated 2016-02-02

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>

Diff between reservoir versions 1.1.3 dated 2016-02-02 and 1.1.4 dated 2016-02-10

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More information about reservoir at CRAN
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Package rcrossref updated to version 0.5.2 with previous version 0.5.0 dated 2016-01-20

Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Ted Hart [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rcrossref versions 0.5.0 dated 2016-01-20 and 0.5.2 dated 2016-02-10

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Package nodiv updated to version 1.1.4 with previous version 1.1.3 dated 2016-02-07

Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>

Diff between nodiv versions 1.1.3 dated 2016-02-07 and 1.1.4 dated 2016-02-10

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Package gmwm updated to version 2.0.0 with previous version 1.0.0 dated 2015-11-06

Title: Generalized Method of Wavelet Moments
Description: Generalized Method of Wavelet Moments (GMWM) is an estimation technique for the parameters of time series models. It uses the wavelet variance in a moment matching approach that makes it particularly suitable for the estimation of certain state-space models. Furthermore, there exists a robust implementation of GMWM, which allows the robust estimation of some state-space models and ARIMA models. Lastly, the package provides the ability to quickly generate time series data, perform different wavelet decompositions, and visualizations.
Author: James Balamuta [aut, cph], Stephane Guerrier [ctb, cre, cph], Roberto Molinari [ctb, cph], Wenchao Yang [ctb]
Maintainer: Stephane Guerrier <stephane@illinois.edu>

Diff between gmwm versions 1.0.0 dated 2015-11-06 and 2.0.0 dated 2016-02-10

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 gmwm-2.0.0/gmwm/NAMESPACE                                                      |   45 
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Package equivalence updated to version 0.7.1 with previous version 0.7.0 dated 2015-07-25

Title: Provides Tests and Graphics for Assessing Tests of Equivalence
Description: Provides statistical tests and graphics for assessing tests of equivalence. Such tests have similarity as the alternative hypothesis instead of the null. Sample data sets are included.
Author: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>
Maintainer: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>

Diff between equivalence versions 0.7.0 dated 2015-07-25 and 0.7.1 dated 2016-02-10

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Package EBMAforecast updated to version 0.52 with previous version 0.42 dated 2013-02-25

Title: Ensemble BMA Forecasting
Description: Ensemble BMA for social science data.
Author: Jacob M. Montgomery, Florian M. Hollenbach, and Michael D. Ward
Maintainer: Florian M. Hollenbach <fhollenbach@tamu.edu>

Diff between EBMAforecast versions 0.42 dated 2013-02-25 and 0.52 dated 2016-02-10

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Package cardioModel updated to version 1.3 with previous version 1.2 dated 2015-09-28

Title: Cardiovascular Safety Exposure-Response Modeling in Early-Phase Clinical Studies
Description: Includes 100 mixed-effects model structures describing the relationship between drug concentration and QT interval, heart rate/pulse rate or blood pressure. Given an exposure-response dataset, the tool fits each model structure to the observed data.
Author: Daniela J Conrado [aut, cre], Gregory J Hather [aut], William S Denney [aut], Danny Chen [ctb]
Maintainer: Daniela J Conrado <danielac@metrumrg.com>

Diff between cardioModel versions 1.2 dated 2015-09-28 and 1.3 dated 2016-02-10

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More information about cardioModel at CRAN
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Package BIOdry updated to version 0.3 with previous version 0.2 dated 2015-12-30

Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel data frames of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in functions ringApply(), modelFrame(), and muleMan().
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Maintainer: Wilson Lara <wilarhen@gmail.com>

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Tue, 09 Feb 2016

Package StMoMo updated to version 0.3.1 with previous version 0.3.0 dated 2015-10-13

Title: Stochastic Mortality Modelling
Description: Implementation of the family of generalised age-period-cohort stochastic mortality models. This family of models encompasses many models proposed in the actuarial and demographic literature including the Lee-Carter model and the Cairns-Blake-Dowd model. It includes functions for fitting mortality models, analysing their goodness-of-fit and performing mortality projections and simulations.
Author: Andres Villegas <andresmauriciovillegas@gmail.com>, Pietro Millossovich <Pietro.Millossovich.1@city.ac.uk>, Vladimir Kaishev <Vladimir.Kaishev.1@city.ac.uk>
Maintainer: Andres Villegas <andresmauriciovillegas@gmail.com>

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Package selectiveInference updated to version 1.1.3 with previous version 1.1.2 dated 2015-12-27

Title: Tools for Post-Selection Inference
Description: New tools for post-selection inference, for use with forward stepwise regression, least angle regression, the lasso, and the many means problem.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor, Joshua Loftus, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>

Diff between selectiveInference versions 1.1.2 dated 2015-12-27 and 1.1.3 dated 2016-02-09

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Package NPBayesImpute updated to version 0.6 with previous version 0.5 dated 2015-03-23

Title: Non-Parametric Bayesian Multiple Imputation for Categorical Data
Description: These routines create multiple imputations of missing at random categorical data, with or without structural zeros. Imputations are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Quanli Wang <quanli@stat.duke.edu>

Diff between NPBayesImpute versions 0.5 dated 2015-03-23 and 0.6 dated 2016-02-09

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Package gitlabr updated to version 0.6.4 with previous version 0.6.2 dated 2016-01-20

Title: Access to the Gitlab API
Description: Provides R functions to access the API of the project and repository management web application gitlab. For many common tasks (repository file access, issue assignment and status, commenting) convenience wrappers are provided, and in addition the full API can be used by specifying request locations. Gitlab is open-source software and can be self-hosted or used on gitlab.com.
Author: Jirka Lewandowski [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>

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More information about gitlabr at CRAN
Permanent link

New package fastGraph with initial version 1.0
Package: fastGraph
Type: Package
Title: Fast Drawing and Shading of Graphs of Statistical Distributions
Version: 1.0
Date: 2016-02-08
Author: Steven T. Garren [aut, cre]
Maintainer: Steven T. Garren <garrenst@jmu.edu>
Description: Provides functionality to produce graphs of probability density functions and cumulative distribution functions with few keystrokes, allows shading under the curve of the probability density function to illustrate concepts such as p-values and critical values, and fits a simple linear regression line on a scatter plot with the equation as the main title.
License: GPL-3
Depends: R (>= 2.0)
NeedsCompilation: no
Packaged: 2016-02-09 17:56:37 UTC; garrenst
Repository: CRAN
Date/Publication: 2016-02-09 20:53:58

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Package cooccur updated to version 1.3 with previous version 1.2 dated 2014-11-18

Title: Probabilistic Species Co-Occurrence Analysis in R
Description: This R package applies the probabilistic model of species co-occurrence (Veech 2013) to a set of species distributed among a set of survey or sampling sites. The algorithm calculates the observed and expected frequencies of co-occurrence between each pair of species. The expected frequency is based on the distribution of each species being random and independent of the other species. The analysis returns the probabilities that a more extreme (either low or high) value of co-occurrence could have been obtained by chance. The package also includes functions for visualizing species co-occurrence results and preparing data for downstream analyses.
Author: Daniel M. Griffith, Joseph A. Veech, and Charles J. Marsh
Maintainer: Daniel M. Griffith <griffith.dan@gmail.com>

Diff between cooccur versions 1.2 dated 2014-11-18 and 1.3 dated 2016-02-09

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New package soc.ca with initial version 0.7.3
Package: soc.ca
Title: Specific Correspondence Analysis for the Social Sciences
Description: Specific and class specific multiple correspondence analysis on survey-like data. Soc.ca is optimized to the needs of the social scientist and presents easily interpretable results in near publication ready quality.
URL: https://github.com/Rsoc/soc.ca
Version: 0.7.3
Maintainer: Anton Grau Larsen <agl.dbp@cbs.dk>
Author: Anton Grau Larsen, with contributions from Christoph Ellersgaard and Stefan Andrade
Depends: R (>= 2.15.0), ggplot2
Imports: gridExtra, ellipse, stats, utils, shiny, reshape2, ggrepel
License: GPL-3
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-02-09 14:23:32 UTC; grau
Repository: CRAN
Date/Publication: 2016-02-09 15:53:12

More information about soc.ca at CRAN
Permanent link

Package rockchalk updated to version 1.8.98 with previous version 1.8.92 dated 2015-02-13

Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation of regression analysis. These functions are used to produce the statistics lectures in http://pj.freefaculty.org/guides. Includes regression diagnostics, regression tables, and plots of interactions and "moderator" variables. The emphasis is on "mean-centered" and "residual-centered" predictors. The vignette "rockchalk" offers a fairly comprehensive overview. The vignette "Rstyle" has advice about coding in R. The package title "rockchalk" refers to our school motto, "Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson <pauljohn@ku.edu>
Maintainer: Paul E. Johnson <pauljohn@ku.edu>

Diff between rockchalk versions 1.8.92 dated 2015-02-13 and 1.8.98 dated 2016-02-09

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Package FMP updated to version 1.4 with previous version 1.3 dated 2016-02-05

Title: Filtered Monotonic Polynomial IRT Models
Description: Estimates Filtered Monotonic Polynomial IRT Models as described by Liang and Browne (2015) <DOI:10.3102/1076998614556816>.
Author: Niels G. Waller <nwaller@umn.edu>
Maintainer: Niels G. Waller <nwaller@umn.edu>

Diff between FMP versions 1.3 dated 2016-02-05 and 1.4 dated 2016-02-09

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Permanent link

New package Watersheds with initial version 1.1
Package: Watersheds
Type: Package
Title: Spatial Watershed Aggregation and Spatial Drainage Network Analysis
Version: 1.1
Date: 2016-02-08
Author: J.A. Torres-Matallana
Maintainer: J. A. Torres-Matallana <arturo.torres@list.lu>
Description: Methods for watersheds aggregation and spatial drainage network analysis.
License: GPL (>= 2)
Depends: R (>= 2.10), methods, sp, maptools, rgeos, lattice, splancs
Packaged: 2016-02-08 14:03:40 UTC; arturo.torres
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-02-09 14:36:29

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Permanent link

Package latticeExtra updated to version 0.6-28 with previous version 0.6-26 dated 2013-08-15

Title: Extra Graphical Utilities Based on Lattice
Description: Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.
Author: Deepayan Sarkar <deepayan.sarkar@r-project.org>, Felix Andrews <felix@nfrac.org>
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>

Diff between latticeExtra versions 0.6-26 dated 2013-08-15 and 0.6-28 dated 2016-02-09

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New package loe with initial version 1.1
Package: loe
Type: Package
Title: Local Ordinal Embedding
Version: 1.1
Date: 2016-02-09
Author: Yoshikazu Terada, Ulrike von Luxburg
Maintainer: Yoshikazu Terada <terada@nict.go.jp>
Depends: R (>= 3.2.3), MASS
Suggests: igraph, Matrix, vegan
Description: Local Ordinal embedding (LOE) is one of graph embedding methods for unweighted graphs.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-02-09 10:40:11 UTC; terada
Repository: CRAN
Date/Publication: 2016-02-09 14:36:35

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New package Compositional with initial version 1.0
Package: Compositional
Version: 1.0
Date: 2016-02-05
Title: Compositional Data Analysis
Authors@R: c(person("Michail", "Tsagris", role = c("aut", "cre"), email = "mtsagris@yahoo.gr"), person("Giorgos", "Athineou", role = "aut", email = "athineou@csd.uoc.gr") )
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Depends: R (>= 3.2.2)
Imports: sn, quantreg, mixture, BB, doParallel, parallel, foreach, MASS
Description: A collection of R functions for compositional data analysis.
License: GPL (>= 2)
URL:
NeedsCompilation: no
Packaged: 2016-02-09 10:19:03 UTC; user
Repository: CRAN
Date/Publication: 2016-02-09 14:36:25

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Package surveillance updated to version 1.11.0 with previous version 1.10-0 dated 2015-11-06

Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
Description: Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hhle and Paul (2008) . A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2014) . For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. 'hhh4' estimates models for (multivariate) count time series following Paul and Held (2011) and Meyer and Held (2014) . 'twinSIR' models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hhle (2009) . 'twinstim' estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) . A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2015) .
Author: Michael Hhle [aut, ths], Sebastian Meyer [aut, cre], 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], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb] (A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <Sebastian.Meyer@ifspm.uzh.ch>

Diff between surveillance versions 1.10-0 dated 2015-11-06 and 1.11.0 dated 2016-02-09

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More information about surveillance at CRAN
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Package svglite updated to version 1.1.0 with previous version 1.0.0 dated 2015-12-08

Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut, cre], T Jake Luciani [aut], Matthieu Decorde [aut], Vaudor Lise [aut], Tony Plate [ctb] (Early line dashing code), David Gohel [ctb] (Line dashing code and raster code), Yixuan Qiu [ctb] (Improved styles; polypath implementation), Håkon Malmedal [ctb] (Opacity code), RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Permanent link

Package Sim.DiffProc updated to version 3.2 with previous version 3.1 dated 2015-12-31

Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>

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Package rorcid updated to version 0.2.2 with previous version 0.2.0 dated 2015-12-07

Title: Interface to the 'Orcid.org' 'API'
Description: Client for the 'Orcid.org' 'API' (http://orcid.org/). Functions included for searching for people, searching by 'DOI', and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rorcid versions 0.2.0 dated 2015-12-07 and 0.2.2 dated 2016-02-09

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Package rangemodelR updated to version 1.0 with previous version 0.1 dated 2015-12-03

Title: Mid-Domain Effect and Species Richness Patterns
Description: Generates expected values of species richness, with continuous or scattered ranges, for data across one or two dimensions.
Author: Aniruddha Marathe, ATREE, Bangalore
Maintainer: Aniruddha Marathe <aniruddha.pravin.marathe@gmail.com>

Diff between rangemodelR versions 0.1 dated 2015-12-03 and 1.0 dated 2016-02-09

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New package iemisc with initial version 0.5.0
Package: iemisc
Title: Irucka Embry's Miscellaneous Functions
Version: 0.5.0
Author: Irucka Embry [aut, cre]. Includes R source code and/or documentation previously published by: Felix Andrews (zoo) and Hans Werner Borchers (pracma). [Borrowed from DescTools description.]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Depends: R (>= 3.0.0), stats, data.table (>= 1.9.4)
Imports: zoo, pracma
Suggests: iemiscdata, Rcpp (>= 0.11.5), RcppOctave, rSymPy, NISTunits, import, financial, optiRum
Description: A collection of Irucka Embry's miscellaneous functions (Engineering Economics, Environmental/Water Resources Engineering, Geometry, Statistics, GNU Octave length functions, etc.).
URL: https://gitlab.com/iembry/iemisc
BugReports: https://gitlab.com/iembry/iemisc/issue
License: GPL (>= 3)
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-02-09 01:56:47 UTC; uoxyh
Repository: CRAN
Date/Publication: 2016-02-09 09:46:48

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New package FamEvent with initial version 1.0
Package: FamEvent
Type: Package
Title: Simulation of Time-to-Event Family Data and Penetrance Estimation
Version: 1.0
Date: 2016-02-08
Author: Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Maintainer: Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
Description: Generates time-to-event family data associated with mutated genes arising from various family study designs such as population-based, clinic- based, or multi-stage designs and provides functions to fit family data accounting for the study design and estimate age-dependent penetrance functions. It also provides carrier probabilities for those with missing genotypes and penetrance estimations are based on an Expectation-Maximization algorithm when genotypes are missing.
License: GPL (>= 2.0)
NeedsCompilation: no
Depends: R(>= 3.0.0), base, MASS, truncnorm, survival, kinship2
Repository: CRAN
Packaged: 2016-02-08 23:09:43 UTC; yunheechoi
Date/Publication: 2016-02-09 09:46:38

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Package dti updated to version 1.2-4.1 with previous version 1.2-4 dated 2016-02-02

Title: Analysis of Diffusion Weighted Imaging (DWI) Data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data. The functionality includes diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), modeling for high angular resolution diffusion weighted imaging (HARDI) using Q-ball-reconstruction and tensor mixture models, several methods for structural adaptive smoothing including POAS and msPOAS, and a streamline fiber tracking for tensor and tensor mixture models. The package provides functionality to manipulate and visualize results in 2D and 3D.
Author: Karsten Tabelow [aut, cre], Joerg Polzehl [aut], Felix Anker [ctb]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>

Diff between dti versions 1.2-4 dated 2016-02-02 and 1.2-4.1 dated 2016-02-09

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Package DDD updated to version 3.2 with previous version 3.1 dated 2016-01-19

Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>. Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence. See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>. Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

Diff between DDD versions 3.1 dated 2016-01-19 and 3.2 dated 2016-02-09

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Package cancerTiming updated to version 3.1.5 with previous version 3.1.3 dated 2016-01-04

Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom <epurdom@stat.berkeley.edu>

Diff between cancerTiming versions 3.1.3 dated 2016-01-04 and 3.1.5 dated 2016-02-09

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Package alphashape3d updated to version 1.2 with previous version 1.1 dated 2014-05-23

Title: Implementation of the 3D Alpha-Shape for the Reconstruction of 3D Sets from a Point Cloud
Description: Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space. The alpha-shape generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of points taken into it. Besides the computation of the alpha-shape, this package provides users with functions to compute the volume of the alpha-shape, identify the connected components and facilitate the three-dimensional graphical visualization of the estimated set.
Author: Thomas Lafarge, Beatriz Pateiro-Lopez
Maintainer: Beatriz Pateiro-Lopez <beatriz.pateiro@usc.es>

Diff between alphashape3d versions 1.1 dated 2014-05-23 and 1.2 dated 2016-02-09

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Package ahp updated to version 0.2.8 with previous version 0.2.7 dated 2016-02-02

Title: Analytic Hierarchy Process
Description: Model and analyse complex decision making problems using the Analytic Hierarchy Process (AHP) by Thomas Saaty.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>

Diff between ahp versions 0.2.7 dated 2016-02-02 and 0.2.8 dated 2016-02-09

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Mon, 08 Feb 2016

Package yCrypticRNAs updated to version 0.99.2 with previous version 0.99.1 dated 2016-01-08

Title: Cryptic Transcription Analysis in Yeast
Description: Calculates cryptic scores for genes using the ratio (Cheung et al., 2008), the 3' enrichment method (DeGennaro et al., 2013) and the probabilistic method. It also provide methods to estimates cryptic transcription start sites.
Author: Nicole Uwimana, Benjamin Haibe-Kains, Francois Robert
Maintainer: Nicole Uwimana <nicole.uwimana@gmail.com>

Diff between yCrypticRNAs versions 0.99.1 dated 2016-01-08 and 0.99.2 dated 2016-02-08

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Package stripless updated to version 1.0-1 with previous version 1.0 dated 2016-01-30

Title: Structured Trellis Displays Without Strips for Lattice Graphics
Description: For making Trellis-type conditioning plots without strip labels. This is useful for displaying the structure of results from factorial designs and other studies when many conditioning variables would clutter the display with layers of redundant strip labels. Settings of the variables are encoded by layout and spacing in the trellis array and decoded by a separate legend. The functionality is implemented by a single S3 generic strucplot() function that is a wrapper for the Lattice package's xyplot() function. This allows access to all Lattice graphics capabilities in the usual way.
Author: Bert Gunter [aut, cre]
Maintainer: Bert Gunter <bgunter@comcast.net>

Diff between stripless versions 1.0 dated 2016-01-30 and 1.0-1 dated 2016-02-08

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New package stpm with initial version 1.0
Package: stpm
Type: Package
Title: Stochastic Model for Analysis of Longitudinal Data
Version: 1.0
Date: 2016-02-08
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Description: Utilities to estimate parameters of stochastic process and modeling survival trajectories and time-to-event outcomes observed from longitudinal studies. Miscellaneous function for data preparation is also provided. For more information, see: "Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al, 2007, Mathematical Biosciences, 208(2), 538-551 <DOI:10.1016/j.mbs.2006.11.006>.
License: GPL
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp,RcppArmadillo
Depends: mice,sas7bdat,stats,nloptr,tools
Suggests: knitr (>= 1.11)
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-02-08 17:00:26 UTC; ilya
Repository: CRAN
Date/Publication: 2016-02-09 00:05:00

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Package rqPen updated to version 1.3 with previous version 1.2 dated 2015-10-22

Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb]
Maintainer: Ben Sherwood <bsherwo2@jhu.edu>

Diff between rqPen versions 1.2 dated 2015-10-22 and 1.3 dated 2016-02-08

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Package rmp updated to version 2.0 with previous version 1.0 dated 2013-04-17

Title: Rounded Mixture Package. Performs Probability Mass Function Estimation with Nonparametric Mixtures of Rounded Kernels
Description: Performs probability mass function estimation with nonparametric mixtures of rounded kernels.
Author: Antonio Canale [aut,cre], Nicola Lunardon [ctb]
Maintainer: Antonio Canale <antonio.canale@unito.it>

Diff between rmp versions 1.0 dated 2013-04-17 and 2.0 dated 2016-02-08

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Package munfold updated to version 0.3.5 with previous version 0.3.4 dated 2016-02-07

Title: Metric Unfolding
Description: Multidimensional unfolding using Schoenemann's algorithm for metric and Procrustes rotation of unfolding results.
Author: Martin Elff
Maintainer: Martin Elff <martin@elff.eu>

Diff between munfold versions 0.3.4 dated 2016-02-07 and 0.3.5 dated 2016-02-08

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New package LCMCR with initial version 0.4
Package: LCMCR
Type: Package
Title: Bayesian Nonparametric Latent-Class Capture-Recapture
Version: 0.4
Date: 2016-02-07
Author: Daniel Manrique-Vallier
Description: Bayesian population size estimation using non parametric latent-class models.
Maintainer: Daniel Manrique-Vallier <dmanriqu@indiana.edu>
License: GPL (>= 2)
Depends: R (>= 3.0.1)
Imports: methods
SystemRequirements: Gnu Scientific Library version >= 1.12
Packaged: 2016-02-08 16:37:06 UTC; d
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-02-08 23:57:11

More information about LCMCR at CRAN
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Package GWRM updated to version 2.1.0.1 with previous version 2.0 dated 2015-04-21

Title: Generalized Waring Regression Model for Count Data
Description: Statistical functions to fit, validate and describe a Generalized Waring Regression Model (GWRM).
Author: Antonio Jose Saez-Castillo [aut, cre], Silverio Vilchez-Lopez [aut], Maria Jose Olmo-Jimenez [aut], Jose Rodriguez-Avi [aut], Antonio Conde-Sanchez [aut], Ana Maria Martinez-Rodriguez [aut]
Maintainer: Antonio Jose Saez-Castillo <ajsaez@ujaen.es>

Diff between GWRM versions 2.0 dated 2015-04-21 and 2.1.0.1 dated 2016-02-08

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New package guess with initial version 0.1
Package: guess
Title: Adjust Estimates of Learning for Guessing
Version: 0.1
Authors@R: c(person("Gaurav", "Sood", email = "gsood07@gmail.com", role = c("aut", "cre")), person("Ken", "Cor", email = "mcor@ualberta.ca", role = c("aut")))
Maintainer: Gaurav Sood <gsood07@gmail.com>
Description: Adjust Estimates of Learning for Guessing. The package provides standard guessing correction, and a latent class model that leverages informative pre-post transitions. For details of the latent class model, see <http://gsood.com/research/papers/guess.pdf>.
URL: http://github.com/soodoku/guess
BugReports: http://github.com/soodoku/guess/issues
Depends: R (>= 3.2.1)
Imports: Rsolnp
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Suggests: knitr (>= 1.11), rmarkdown, testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-02-08 21:35:52 UTC; gaurav
Author: Gaurav Sood [aut, cre], Ken Cor [aut]
Repository: CRAN
Date/Publication: 2016-02-08 23:44:06

More information about guess at CRAN
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Package ClusterStability updated to version 1.0.3 with previous version 1.0.2 dated 2015-10-14

Title: Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Matthieu Willems, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>

Diff between ClusterStability versions 1.0.2 dated 2015-10-14 and 1.0.3 dated 2016-02-08

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New package permubiome with initial version 1.0
Package: permubiome
Type: Package
Title: A Permutation Based Test for Biomarker Discovery in Microbiome Data
Version: 1.0
Date: 2016-02-01
Author: Alfonso Benitez-Paez
Maintainer: Alfonso Benitez-Paez <abenitez@iata.csic.es>
Description: All the functions compiled in this package were created to perform permutation-based non-parametric analysis on microbiome data for biomarker discovery aims. This test executes thousands of comparisons in pairwise manner, after random shuffling of data into the different groups of study.
License: GPL-2
Imports: ggplot2
NeedsCompilation: no
Packaged: 2016-02-08 15:36:38 UTC; alfonso
Repository: CRAN
Date/Publication: 2016-02-08 17:32:13

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Package gamlss updated to version 4.3-8 with previous version 4.3-7 dated 2016-01-05

Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph], Bob Rigby [aut], Vlasios Voudouris [ctb], Calliope Akantziliotou [ctb], Marco Enea [ctb], Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>

Diff between gamlss versions 4.3-7 dated 2016-01-05 and 4.3-8 dated 2016-02-08

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Package sjPlot updated to version 1.9.1 with previous version 1.9 dated 2016-01-26

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjPlot versions 1.9 dated 2016-01-26 and 1.9.1 dated 2016-02-08

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Package robCompositions updated to version 2.0.0 with previous version 1.9.1 dated 2015-05-06

Title: Robust Estimation for Compositional Data
Description: Methods for analysis of compositional data including robust methods, imputation, methods to replace rounded zeros, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.
Author: Matthias Templ, Karel Hron, Peter Filzmoser
Maintainer: Matthias Templ <templ@tuwien.ac.at>

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Package matlib updated to version 0.7.2 with previous version 0.7.0 dated 2016-01-06

Title: Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. These functions are mainly for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D.
Author: Michael Friendly [aut, cre], John Fox [aut], Georges Monette [ctb], Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

Diff between matlib versions 0.7.0 dated 2016-01-06 and 0.7.2 dated 2016-02-08

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 NAMESPACE             |    1 +
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 R/corner.R            |    3 ++-
 R/regvec3d.R          |   27 ++++++++++++++++++++++-----
 README.md             |    2 +-
 inst/doc/gramreg.html |   40 ++++++++++++++++++++--------------------
 man/plot.regvec3d.Rd  |   11 ++++++++---
 9 files changed, 75 insertions(+), 44 deletions(-)

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Package ggrepel updated to version 0.5 with previous version 0.4 dated 2016-01-12

Title: Repulsive Text and Label Geoms for 'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.
Author: Kamil Slowikowski [aut, cre]
Maintainer: Kamil Slowikowski <kslowikowski@fas.harvard.edu>

Diff between ggrepel versions 0.4 dated 2016-01-12 and 0.5 dated 2016-02-08

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 ggrepel-0.5/ggrepel/NEWS                                                    |   70 ++
 ggrepel-0.5/ggrepel/R/RcppExports.R                                         |  103 +--
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 ggrepel-0.5/ggrepel/R/geom-text-repel.R                                     |  273 +++++----
 ggrepel-0.5/ggrepel/README.md                                               |   10 
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Package swfscMisc updated to version 1.0.9 with previous version 1.0.6 dated 2015-07-29

Title: Miscellaneous Functions for Southwest Fisheries Science Center
Description: Collection of conversion, analytical, geodesic, mapping, and plotting functions. Used to support packages and code written by researchers at the Southwest Fisheries Science Center of the National Oceanic and Atmospheric Administration.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>

Diff between swfscMisc versions 1.0.6 dated 2015-07-29 and 1.0.9 dated 2016-02-08

 DESCRIPTION               |    9 +--
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 man/convert.angle.Rd      |   10 ++-
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Package spgrass6 updated to version 0.8-9 with previous version 0.8-8 dated 2015-09-28

Title: Interface Between GRASS 6+ Geographical Information System and R
Description: Interpreted interface between GRASS 6+ geographical information system and R, based on starting R from within the GRASS environment, or running free-standing R in a temporary GRASS location; the package provides facilities for using all GRASS commands from the R command line. This package may not be used for GRASS 7, for which rgrass7 should be used.
Author: Roger Bivand [cre, aut], Rainer Krug [ctb], Markus Neteler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between spgrass6 versions 0.8-8 dated 2015-09-28 and 0.8-9 dated 2016-02-08

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 4 files changed, 10 insertions(+), 10 deletions(-)

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Package spc updated to version 0.5.3 with previous version 0.5.2 dated 2015-11-01

Title: Statistical Process Control -- Collection of Some Useful Functions
Description: Evaluation of control charts by means of the zero-state, steady-state ARL (Average Run Length) and RL quantiles. Setting up control charts for given in-control ARL. The control charts under consideration are one- and two-sided EWMA, CUSUM, and Shiryaev-Roberts schemes for monitoring the mean of normally distributed independent data. ARL calculation of the same set of schemes under drift are added. Other charts and parameters are in preparation. Further SPC areas will be covered as well (sampling plans, capability indices ...).
Author: Sven Knoth
Maintainer: Sven Knoth <Sven.Knoth@gmx.de>

Diff between spc versions 0.5.2 dated 2015-11-01 and 0.5.3 dated 2016-02-08

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New package robotstxt with initial version 0.1.2
Package: robotstxt
Type: Package
Title: A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker
Version: 0.1.2
Authors@R: c(person("Peter", "Meissner", role = c("aut", "cre"), email = "retep.meissner@gmail.com"), person("Oliver", "Keys", role = "ctb"))
Description: Provides a 'Robotstxt' ('R6') class and accompanying methods to parse and check 'robots.txt' files. Data fields are provided as data frames and vectors. Permissions can be checked by providing path character vectors and optional bot names.
License: MIT + file LICENSE
LazyData: TRUE
BugReports: https://github.com/petermeissner/robotstxt/issues
URL: https://github.com/petermeissner/robotstxt
Imports: R6 (>= 2.1.1), stringr (>= 1.0.0), httr (>= 1.0.0)
Suggests: knitr, rmarkdown, dplyr, testthat
Depends: R (>= 3.0.0)
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-02-07 23:21:42 UTC; peter
Author: Peter Meissner [aut, cre], Oliver Keys [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Repository: CRAN
Date/Publication: 2016-02-08 13:37:57

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Package rfPermute updated to version 1.9.3 with previous version 1.9.2 dated 2015-07-29

Title: Estimate Permutation p-Values for Random Forest Importance Metrics
Description: Estimate significance of importance metrics for a Random Forest model by permuting the response variable. Produces null distribution of importance metrics for each predictor variable and p-value of observed.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>

Diff between rfPermute versions 1.9.2 dated 2015-07-29 and 1.9.3 dated 2016-02-08

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 NEWS.md                   |   12 ++++++++++++
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Package overlapping updated to version 1.2 with previous version 1.1 dated 2016-01-08

Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more empirical distributions.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>

Diff between overlapping versions 1.1 dated 2016-01-08 and 1.2 dated 2016-02-08

 DESCRIPTION |   10 +++++-----
 MD5         |    4 ++--
 NEWS        |    6 +++++-
 3 files changed, 12 insertions(+), 8 deletions(-)

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Package move updated to version 1.6.541 with previous version 1.6.539 dated 2016-02-02

Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in movebank.org as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Author: Bart Kranstauber <bart.kranstauber@uni-konstanz.de>, Marco Smolla <marco.smolla@postgrad.manchester.ac.uk>
Maintainer: Bart Kranstauber <bart.kranstauber@uni-konstanz.de>

Diff between move versions 1.6.539 dated 2016-02-02 and 1.6.541 dated 2016-02-08

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 DESCRIPTION                          |    6 +++---
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 inst/doc/move.pdf                    |binary
 tests/testthat/test.smallFunctions.R |    4 ++--
 6 files changed, 14 insertions(+), 10 deletions(-)

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