Thu, 27 Jul 2017

Package windfarmGA updated to version 1.1.1 with previous version 1.1 dated 2017-07-09

Title: Genetic Algorithm for Wind Farm Layout Optimization
Description: The genetic algorithm is designed to optimize small wind farms consisting of up to 50 turbines. The algorithm works with a fixed amount of turbines, a fixed rotor radius and a mean wind speed value for every incoming wind direction. If required, it can include a terrain effect model which downloads an 'SRTM' elevation model automatically and loads a Corine Land Cover raster, which has to be downloaded previously. Further information can be found in the description of the function 'windfarmGA'. To start an optimization run, either the function 'windfarmGA' or 'genAlgo' can be used. The function 'windfarmGA' checks the user inputs interactively and then runs the function 'genAlgo'. If the input parameters are already known, an optimization can be run directly via the function 'genAlgo'. Their output is identical.
Author: Sebastian Gatscha
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>

Diff between windfarmGA versions 1.1 dated 2017-07-09 and 1.1.1 dated 2017-07-27

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Package stringdist updated to version 0.9.4.5 with previous version 0.9.4.4 dated 2016-12-16

Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.
Author: Mark van der Loo [aut, cre], Jan van der Laan [ctb], R Core Team [ctb], Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

Diff between stringdist versions 0.9.4.4 dated 2016-12-16 and 0.9.4.5 dated 2017-07-27

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Package rsdmx updated to version 0.5-9 with previous version 0.5-8 dated 2017-02-21

Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents exchanged through the Statistical Data and Metadata Exchange (SDMX) framework, currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre], Matthieu Stigler [ctb], Eric Persson [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Diff between rsdmx versions 0.5-8 dated 2017-02-21 and 0.5-9 dated 2017-07-27

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New package optiSolve with initial version 0.1
Package: optiSolve
Type: Package
Title: Linear, Quadratic, and Rational Optimization
Version: 0.1
Date: 2017-07-27
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Depends: R (>= 3.3.2)
Description: Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'. Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp', or transformed into semidefinite programming problems and solved using solver 'csdp'.
License: GPL-2
Imports: Matrix, shapes, Rcsdp, alabama, cccp, nloptr, MASS, methods, plyr, stringr, stats, Rcpp (>= 0.12.4)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-27 08:33:15 UTC; Robin
Repository: CRAN
Date/Publication: 2017-07-27 22:22:13 UTC

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Package diagis updated to version 0.1.3 with previous version 0.1.2 dated 2017-05-22

Title: Diagnostic Plot and Multivariate Summary Statistics of Weighted Samples from Importance Sampling
Description: Fast functions for effective sample size, weighted multivariate mean and variance computation, and weight diagnostic plot for generic importance sampling type results.
Author: Jouni Helske
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between diagis versions 0.1.2 dated 2017-05-22 and 0.1.3 dated 2017-07-27

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Package dad updated to version 3.0.0 with previous version 2.0.0 dated 2016-12-16

Title: Three-Way Data Analysis Through Densities
Description: The three-way data consists of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides tools to manage such data and functional methods (principal component analysis, multidimensional scaling, cluster analysis, discriminant analysis...) for such probability densities.
Author: Rachid Boumaza[aut, cre], Pierre Santagostini [aut], Smail Yousfi [aut], Gilles Hunault [ctb], Julie Bourbeillon [ctb], Besnik Pumo [ctb], Sabine Demotes-Mainard [aut]
Maintainer: Rachid Boumaza <rachid.boumaza@agrocampus-ouest.fr>

Diff between dad versions 2.0.0 dated 2016-12-16 and 3.0.0 dated 2017-07-27

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New package CrossValidate with initial version 2.3.0
Package: CrossValidate
Version: 2.3.0
Date: 2017-07-24
Title: Classes and Methods for Cross Validation of "Class Prediction" Algorithms
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Depends: R (>= 3.0), Modeler
Imports: methods, oompaBase (>= 3.0.1)
Suggests: Biobase
Description: Defines classes and methods to cross-validate various binary classification algorithms used for "class prediction" problems.
License: Apache License (== 2.0)
LazyLoad: yes
biocViews: Microarray, Clustering
URL: http://oompa.r-forge.r-project.org
NeedsCompilation: no
Packaged: 2017-07-27 19:40:54 UTC; coom05
Repository: CRAN
Date/Publication: 2017-07-27 22:23:16 UTC

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Package tidyquant updated to version 0.5.2 with previous version 0.5.1 dated 2017-04-24

Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between tidyquant versions 0.5.1 dated 2017-04-24 and 0.5.2 dated 2017-07-27

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Package textshape updated to version 1.3.0 with previous version 1.0.2 dated 2017-02-22

Title: Tools for Reshaping Text
Description: Tools that can be used to reshape and restructure text data.
Author: Tyler Rinker [aut, cre], Joran Elias [ctb], Matthew Flickinger [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between textshape versions 1.0.2 dated 2017-02-22 and 1.3.0 dated 2017-07-27

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Package tensorflow updated to version 1.3 with previous version 0.9 dated 2017-06-25

Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
Author: JJ Allaire [aut, cre], RStudio [cph, fnd], Yuan Tang [aut, cph], Dirk Eddelbuettel [ctb, cph], Nick Golding [ctb, cph], Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package relsurv updated to version 2.1 with previous version 2.0-9 dated 2016-04-25

Title: Relative Survival
Description: Various functions for relative survival analysis.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>

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Package plotmo updated to version 3.3.4 with previous version 3.3.3 dated 2017-05-05

Title: Plot a Model's Response and Residuals
Description: Plot model surfaces for a wide variety of models using partial dependence plots and other techniques. Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package officer updated to version 0.1.5 with previous version 0.1.4 dated 2017-06-06

Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R. The package focus on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. When working with 'PowerPoint' presentations, slides can be added or removed; shapes inside slides can also be added or removed. When working with 'Word' documents, a cursor can be used to help insert or delete content at a specific location in the document. The package does not require any installation of Microsoft product to be able to write Microsoft files.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package FSA updated to version 0.8.14 with previous version 0.8.13 dated 2017-04-29

Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>

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Package dHSIC updated to version 2.0 with previous version 1.1 dated 2017-06-01

Title: Independence Testing via Hilbert Schmidt Independence Criterion
Description: Contains an implementation of the d-variable Hilbert Schmidt independence criterion and several hypothesis tests based on it, as described in Pfister et al. (2017) <doi:10.1111/rssb.12235>.
Author: Niklas Pfister and Jonas Peters
Maintainer: Niklas Pfister <pfister@stat.math.ethz.ch>

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Package ChemoSpec updated to version 4.4.85 with previous version 4.4.17 dated 2017-02-13

Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson [aut, cre], Mike Bostock [cph, ctb] (author of the d3.js library used in plotSpectraJS, http://d3js.org)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

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Package rxylib updated to version 0.2.0 with previous version 0.1.1 dated 2017-07-08

Title: Import XY-Data into R
Description: Provides access to the 'xylib' C library for to import xy data from powder diffraction, spectroscopy and other experimental methods.
Author: Sebastian Kreutzer [aut, trl, cre], Johannes Friedrich [aut], RLum Team [ctb], Marcin Wojdyr [cph] (C++ library 'xylib'), Peng Zhang [cph] (C++ library 'xylib')
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>

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Package fastR updated to version 0.10.3 with previous version 1.1 dated 2016-07-07

Title: Foundations and Applications of Statistics Using R
Description: Data sets and utilities to accompany "Foundations and Applications of Statistics: an Introduction using R" (R Pruim, published by AMS, 2011), a text covering topics from probability and mathematical statistics at an advanced undergraduate level. R is integrated throughout, and access to all the R code in the book is provided via the snippet function.
Author: Randall Pruim
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Package Delta updated to version 0.1.1.11 with previous version 0.1.1.1 dated 2017-06-21

Title: Measure of Agreement Between Two Raters
Description: Measure of agreement Delta was originally by Martín & Femia (2004) <DOI:10.1348/000711004849268>. Since then has been considered as agreement measure for different fields, since their behavior is usually better than the usual Kappa index by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with Delta is that can not be computed by hand contrary to Kappa.
Author: Antonio Rodriguez [aut, cre], Pedro Femia [aut, cph], Antonio Martín [aut, cph]
Maintainer: Antonio Rodriguez <tonirodriguezcontesti@gmail.com>

Diff between Delta versions 0.1.1.1 dated 2017-06-21 and 0.1.1.11 dated 2017-07-27

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Package coda.base updated to version 0.1.4 with previous version 0.1.3 dated 2017-07-18

Title: A Basic Set of Functions for Compositional Data Analysis
Description: A minimum set of functions to perform compositional data analysis using the log-ratio approach introduced by John Aitchison in 1982. Main functions have been implemented in c++ for better performance.
Author: Marc Comas-Cufí [aut, cre]
Maintainer: Marc Comas-Cufí <mcomas@imae.udg.edu>

Diff between coda.base versions 0.1.3 dated 2017-07-18 and 0.1.4 dated 2017-07-27

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Package coga updated to version 0.2.1 with previous version 0.2.0 dated 2017-06-28

Title: Convolution of Gamma Distributions
Description: Convolution of gamma distributions in R. The convolution of gamma distributions is the sum of series of gamma distributions and all gamma distributions here can have different parameters. This package can calculate density, distribution function and do simulation work.
Author: Chaoran Hu [aut, cre], Vladimir Pozdnyakov [ths], Jun Yan [ths]
Maintainer: Chaoran Hu <chaoran.hu@uconn.edu>

Diff between coga versions 0.2.0 dated 2017-06-28 and 0.2.1 dated 2017-07-27

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Package clustMixType updated to version 0.1-22 with previous version 0.1-17 dated 2016-11-11

Title: k-Prototypes Clustering for Mixed Variable-Type Data
Description: Functions to perform k-prototypes partitioning clustering for mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining and Knowledge Discovery 2, 283-304, <DOI:10.1023/A:1009769707641>.
Author: Gero Szepannek
Maintainer: Gero Szepannek <gero.szepannek@web.de>

Diff between clustMixType versions 0.1-17 dated 2016-11-11 and 0.1-22 dated 2017-07-27

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Package subselect updated to version 0.13 with previous version 0.12-6 dated 2016-07-28

Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima <jcadima@isa.utl.pt>

Diff between subselect versions 0.12-6 dated 2016-07-28 and 0.13 dated 2017-07-27

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New package simsurv with initial version 0.1.0
Package: simsurv
Type: Package
Title: Simulate Survival Data
Version: 0.1.0
Authors@R: c(person("Sam", "Brilleman", email = "sam.brilleman@monash.edu", role = c("cre", "aut", "cph")))
Maintainer: Sam Brilleman <sam.brilleman@monash.edu>
Description: Simulate survival times from standard parametric survival distributions (exponential, Weibull, Gompertz), 2-component mixture distributions, or a user-defined hazard or log hazard function. Baseline covariates can be included under a proportional hazards assumption. Time dependent effects (i.e. non-proportional hazards) can be included by interacting covariates with linear time or some transformation of time. The 2-component mixture distributions can allow for a variety of flexible baseline hazard functions. If the user wishes to provide a user-defined hazard or log hazard function then this is also possible, and the resulting cumulative hazard function does not need to have a closed-form solution. Note that this package is modelled on the 'survsim' package available in the 'Stata' software (see Crowther and Lambert (2012) <http://www.stata-journal.com/sjpdf.html?articlenum=st0275> or Crowther and Lambert (2013) <doi:10.1002/sim.5823>).
License: GPL (>= 3) | file LICENSE
Depends: R (>= 3.3.2)
Imports: methods, stats
Suggests: eha (>= 2.4.5), MASS, survival (>= 2.40.1), testthat (>= 1.0.2)
LazyData: true
BugReports: https://github.com/sambrilleman/simsurv/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-27 04:06:17 UTC; brillems
Author: Sam Brilleman [cre, aut, cph]
Repository: CRAN
Date/Publication: 2017-07-27 11:08:12 UTC

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New package mosaicCalc with initial version 0.5.0
Package: mosaicCalc
Type: Package
Title: Function-Based Numerical and Symbolic Differentiation and Antidifferentiation
Description: Part of the Project MOSAIC (<http://mosaic-web.org/>) suite that provides utility functions for doing calculus (differentiation and integration) in R. The main differentiation and antidifferentiation operators are described using formulas and return functions rather than numerical values. Numerical values can be obtained by evaluating these functions.
Version: 0.5.0
Date: 2017-07-26
Depends: R (>= 3.0.0), mosaicCore
Imports: methods, stats, MASS, mosaic
Suggests: testthat, knitr, rmarkdown
Author: Daniel T. Kaplan <kaplan@macalester.edu>, Randall Pruim <rpruim@calvin.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
URL: https://github.com/ProjectMOSAIC/mosaicCalc
BugReports: https://github.com/ProjectMOSAIC/mosaicCalc/issues
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2017-07-27 11:12:00 UTC; rpruim
Repository: CRAN
Date/Publication: 2017-07-27 11:22:02 UTC

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Package SiMRiv updated to version 1.0.0 with previous version 0.9.1 dated 2016-07-15

Title: Individual-Based, Spatially-Explicit Simulation and Analysis of Multi-State Movements in River Networks and Heterogeneous Landscapes
Description: Provides functions to generate and analyze individual-based spatially-explicit simulations of multi-state movements in heterogeneous landscapes, based on "resistance" rasters. Although originally conceived and designed to simulate spatially-explicit trajectories of species constrained to linear, dendritic habitats (e.g., river networks), the simulation algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism. Thus, the user will be able to use the package to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as mechanistic null models to test e.g. for species site fidelity and other 'Movement Ecology' hypotheses, or for other predictive purposes. The package should thus be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface of animal behaviour, landscape, spatial and movement ecology, disease and invasive species spread, and population dynamics.
Author: Lorenzo Quaglietta [aut], Miguel Porto [aut, cre], Erida Gjini [ctb]
Maintainer: Miguel Porto <mpbertolo@gmail.com>

Diff between SiMRiv versions 0.9.1 dated 2016-07-15 and 1.0.0 dated 2017-07-27

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Package RHMS updated to version 1.3 with previous version 1.2 dated 2017-07-14

Title: Hydrologic Modelling System for R Users
Description: Hydrologic modelling system is an object oriented tool which enables R users to simulate and analyze hydrologic events. The package proposes functions and methods for construction, simulation, visualization, and calibration of hydrologic systems.
Author: Rezgar Arabzadeh ; Shahab Araghinejad
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>

Diff between RHMS versions 1.2 dated 2017-07-14 and 1.3 dated 2017-07-27

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New package recipes with initial version 0.1.0
Package: recipes
Title: Preprocessing Tools to Create Design Matrices
Version: 0.1.0
Authors@R: c( person("Max", "Kuhn", , "max@rstudio.com", c("aut", "cre")), person("Hadley", "Wickham", , "hadley@rstudio.com", "aut"), person("RStudio", role = "cph"))
Description: An extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.
URL: https://github.com/topepo/recipes
BugReports: https://github.com/topepo/recipes/issues
Depends: R (>= 3.2.3), dplyr
Imports: tibble, stats, ipred, dimRed (>= 0.1.0), lubridate, timeDate, ddalpha, purrr, rlang (>= 0.1.1), gower, RcppRoll, tidyselect (>= 0.1.1), magrittr
Suggests: testthat, rpart, kernlab, fastICA, RANN, igraph, knitr, caret, ggplot2, rmarkdown
License: GPL-2
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-27 01:40:39 UTC; max
Author: Max Kuhn [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Repository: CRAN
Date/Publication: 2017-07-27 10:46:19 UTC

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Package preseqR updated to version 3.1.1 with previous version 3.1.0 dated 2017-05-21

Title: Predicting the Number of Species in a Random Sample
Description: The relation between the number of species and the number of individuals in a random sample is a classic problem back to Fisher (1943) <doi:10.2307/1411>. We generalize this problem to estimate the number of species represented at least r times in a random sample. In particular when r=1, it becomes the classic problem. We use a mixture of Poisson processes to model sampling procedures and apply a nonparametric empirical Bayes approach to obtain an estimator. For more information on preseqR, see Deng C, Daley T and Smith AD (2015) <doi:10.1007/s40484-015-0049-7> and Deng C and Smith AD (2016) <arXiv:1607.02804v2>.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng <chaodeng@usc.edu>

Diff between preseqR versions 3.1.0 dated 2017-05-21 and 3.1.1 dated 2017-07-27

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New package lsplsGlm with initial version 1.0
Package: lsplsGlm
Type: Package
Title: Classification using LS-PLS for Logistic Regression
Version: 1.0
Date: 2017-07-19
Encoding: latin1
Author: Caroline Bazzoli <caroline.bazzoli@univ-grenoble-alpes.fr>, Sophie Lambert-Lacroix <sophie.lambert-lacroix@univ-grenoble-alpes.fr>, Thomas Bouleau <tbouleau@gmail.com>
Depends: R (>= 3.0), methods, stats
Maintainer: Bazzoli Caroline <caroline.bazzoli@univ-grenoble-alpes.fr>
Description: Fit logistic regression models using LS-PLS approaches to analyse both clinical and genomic data. (C. Bazzoli and S. Lambert-Lacroix. (2017) Classification using LS-PLS with logistic regression based on both clinical and gene expression variables <https://hal.archives-ouvertes.fr/hal-01405101>).
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
NeedsCompilation: no
Packaged: 2017-07-27 09:55:55 UTC; tbouleau
Repository: CRAN
Date/Publication: 2017-07-27 10:34:54 UTC

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New package icmm with initial version 1.0
Package: icmm
Type: Package
Title: Empirical Bayes Variable Selection via ICM/M Algorithm
Version: 1.0
Authors@R: c(person("Vitara", "Pungpapong", role = c("aut", "cre"), email = "vitara@cbs.chula.ac.th"), person("Min", "Zhang", role = "aut", email="minzhang@stat.purdue.edu"), person("Dabao", "Zhang", role = "aut", email = "zhangdb@stat.purdue.edu"))
Author: Vitara Pungpapong [aut, cre], Min Zhang [aut], Dabao Zhang [aut]
Maintainer: Vitara Pungpapong <vitara@cbs.chula.ac.th>
Description: Carries out empirical Bayes variable selection via ICM/M algorithm. The basic problem is to fit high-dimensional regression which most coefficients are assumed to be zero. This package allows incorporating the Ising prior to capture structure of predictors in the modeling process. The current version of this package can handle the normal, binary logistic, and Cox's regression (Pungpapong et. al. (2015) <doi:10.1214/15-EJS1034>, Pungpapong et. al. (2017) <arXiv:1707.08298>).
License: GPL (>= 2)
Imports: EbayesThresh
Suggests: MASS, stats
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-07-27 08:17:17 UTC; vpungpap
Repository: CRAN
Date/Publication: 2017-07-27 08:42:29 UTC

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Wed, 26 Jul 2017

Package arulesCBA updated to version 1.1.2 with previous version 1.1.1 dated 2017-04-03

Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph], Michael Hahsler [ctb]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>

Diff between arulesCBA versions 1.1.1 dated 2017-04-03 and 1.1.2 dated 2017-07-26

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New package unrepx with initial version 1.0
Package: unrepx
Type: Package
Title: Analysis and Graphics for Unreplicated Experiments
Version: 1.0
Date: 2017-07-26
Authors@R: c(person("Russell", "Lenth", role = c("aut", "cre", "cph"), email = "russell-lenth@uiowa.edu"))
LazyData: yes
BugReports: https://github.com/rvlenth/unrepx/issues
Description: Provides half-normal plots, reference plots, and Pareto plots of effects from an unreplicated experiment, along with various pseudo-standard-error measures, simulated reference distributions, and other tools. Many of these methods are described in Daniel C. (1959) <doi:10.1080/00401706.1959.10489866> and/or Lenth R.V. (1989) <doi:10.1080/00401706.1989.10488595>, but some new approaches are added and integrated in one package.
Suggests: knitr
VignetteBuilder: knitr
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2017-07-26 19:57:05 UTC; rlenth
Author: Russell Lenth [aut, cre, cph]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Repository: CRAN
Date/Publication: 2017-07-26 21:59:28 UTC

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Package table1xls updated to version 0.4.0 with previous version 0.3.2 dated 2016-07-18

Title: Exports Reproducible Summary Tables to Multi-Tab Spreadsheet Files (.xls or .xlsx)
Description: A collection of time-saving wrappers for reproducible export of summary tables commonly used in scientific articles, to .xls/.xlsx multi-tab spreadsheets, while controlling spreadsheet layout. Powered by 'XLConnect'/'rJava' utilities.
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <assaf.oron@seattlechildrens.org>

Diff between table1xls versions 0.3.2 dated 2016-07-18 and 0.4.0 dated 2017-07-26

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New package sdm with initial version 1.0-41
Package: sdm
Type: Package
Title: Species Distribution Modelling
Version: 1.0-41
Date: 2017-07-26
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Depends: methods, sp (>= 1.2-0), R (>= 3.0.0)
Imports: raster
Suggests: rgdal (>= 0.9-1), knitr, shinyBS, shiny, dismo, rmarkdown
Description: An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
License: GPL (>= 3)
URL: http://biogeoinformatics.org
VignetteBuilder: knitr
Repository: CRAN
Repository/R-Forge/Project: sdm
Repository/R-Forge/Revision: 63
Repository/R-Forge/DateTimeStamp: 2017-07-26 18:33:47
Date/Publication: 2017-07-26 22:13:23 UTC
NeedsCompilation: no
Packaged: 2017-07-26 18:46:15 UTC; rforge

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New package mnreadR with initial version 0.1.0
Package: mnreadR
Type: Package
Title: MNREAD Parameters Estimation
Version: 0.1.0
Authors@R: c( person("Aurelie", "Calabrese", email = "acalabre@umn.edu", role = c("aut", "cre")), person("J. Steve", "Mansfield", email = "steve.mansfield@plattsburgh.edu", role = "aut"), person("Gordon E.", "Legge", email = "legge@umn.edu", role = "aut") )
Description: Allows to analyze MNREAD data. The MNREAD Acuity Charts are continuous text reading acuity charts for normal and low vision. Provides the necessary functions to estimate automatically the four MNREAD parameters: Maximum Reading Speed, Critical Print Size, Reading Acuity and Reading Accessibility Index (Calabrese et al (2016) <doi:10.1001/jamaophthalmol.2015.6097>).
Depends: R (>= 2.10), dplyr
Imports: stats
URL: http://legge.psych.umn.edu/mnread-acuity-charts
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-26 20:21:57 UTC; Aurelie
Author: Aurelie Calabrese [aut, cre], J. Steve Mansfield [aut], Gordon E. Legge [aut]
Maintainer: Aurelie Calabrese <acalabre@umn.edu>
Repository: CRAN
Date/Publication: 2017-07-26 22:06:42 UTC

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Package gifti updated to version 0.7.4 with previous version 0.7.1 dated 2017-05-05

Title: Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information
Description: Functions to read in the geometry format under the 'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called 'GIFTI' <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.
Author: John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>

Diff between gifti versions 0.7.1 dated 2017-05-05 and 0.7.4 dated 2017-07-26

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Package ASMap updated to version 1.0-1 with previous version 1.0-0 dated 2017-07-11

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler <dbutler@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>

Diff between ASMap versions 1.0-0 dated 2017-07-11 and 1.0-1 dated 2017-07-26

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Package mirtCAT updated to version 1.6.1 with previous version 1.5 dated 2017-05-04

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests (CAT) using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R. Additionally, optimal test designs (e.g., "shadow testing") are supported for tests which contain a large number of item selection constraints. Finally, package contains tools useful for performing Monte Carlo simulations for studying the behavior of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between mirtCAT versions 1.5 dated 2017-05-04 and 1.6.1 dated 2017-07-26

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Package MCS updated to version 0.1.2 with previous version 0.1.1 dated 2015-03-22

Title: Model Confidence Set Procedure
Description: Perform the model confidence set procedure of Hansen et al (2011).
Author: Leopoldo Catania & Mauro Bernardi
Maintainer: Leopoldo Catania <leopoldo.catania@gmail.com>

Diff between MCS versions 0.1.1 dated 2015-03-22 and 0.1.2 dated 2017-07-26

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New package maxTPR with initial version 0.1.0
Package: maxTPR
Type: Package
Title: Maximizing the TPR for a Specified FPR
Version: 0.1.0
Date: 2017-07-26
Author: Allison Meisner
Maintainer: Allison Meisner <allison.meisner@gmail.com>
Description: Estimates a linear combination of predictors by maximizing a smooth approximation to the estimated true positive rate (TPR; sensitivity) while constraining a smooth approximation to the estimated false positive rate (FPR; 1-specificity) at a user-specified level.
License: GPL-2
LazyData: TRUE
Imports: aucm, Rsolnp
NeedsCompilation: no
Packaged: 2017-07-26 17:53:36 UTC; allison
Repository: CRAN
Date/Publication: 2017-07-26 21:41:21 UTC

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New package loon with initial version 1.1.0
Package: loon
Type: Package
Title: Interactive Statistical Data Visualization
Version: 1.1.0
Date: 2017-07-26
Authors@R: c( person("Adrian", "Waddell", , "adrian@waddell.ch", role = c("aut", "cre")), person("R. Wayne", "Oldford", , "rwoldford@uwaterloo.ca", role = "aut") )
URL: http://waddella.github.io/loon/
Description: An extendable toolkit for interactive data visualization and exploration.
License: GPL-2
Depends: R (>= 3.4.0), methods, tcltk
Imports: tools, graphics, grDevices, utils, stats
Suggests: maps, sp, graph, scagnostics, PairViz, RColorBrewer, RnavGraphImageData, rworldmap, rgl, Rgraphviz, RDRToolbox, kernlab, scales, MASS, dplyr, testthat, knitr, rmarkdown
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-07-26 19:34:25 UTC; adrian
Author: Adrian Waddell [aut, cre], R. Wayne Oldford [aut]
Maintainer: Adrian Waddell <adrian@waddell.ch>
Repository: CRAN
Date/Publication: 2017-07-26 21:51:02 UTC

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Package exCon updated to version 0.2.5 with previous version 0.2.1 dated 2017-01-11

Title: Interactive Exploration of Contour Data
Description: Interactive tools 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. The functions in this package create interactive web pages showing the contoured data, possibly with slices from the original matrix parallel to each dimension. The interactive behavior is created using the 'D3.js' 'JavaScript' library by Mike Bostock.
Author: Bryan A. Hanson [aut, cre], Kristina R. Mulry [ctb], Mike Bostock [cph, ctb] (author of the d3.js library, http://d3js.org)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

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Package Compositional updated to version 2.5 with previous version 2.4 dated 2017-05-29

Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 2.4 dated 2017-05-29 and 2.5 dated 2017-07-26

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New package blandr with initial version 0.4.3
Package: blandr
Title: Bland-Altman Method Comparison
Version: 0.4.3
Description: Carries out Bland Altman analyses (also known as a Tukey mean-difference plot) as described by JM Bland and DG Altman in 1986 <doi:10.1016/S0140-6736(86)90837-8>. This package was created in 2015 as existing Bland-Altman analysis functions did not calculate confidence intervals. This package was created to rectify this, and create reproducible plots.
Depends: R (>= 3.4.0)
Authors@R: person("Deepankar", "Datta", email = "deepankardatta@nhs.net", role = c("aut", "cre"))
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/deepankardatta/blandr/
BugReports: https://github.com/deepankardatta/blandr/issues
Imports: ggplot2, knitr
Suggests: rmarkdown
VignetteBuilder: knitr
Collate: 'blandr.basic.plot.r' 'blandr.data.preparation.r' 'blandr.ggplot.r' 'blandr.plot.limits.r' 'blandr.statistics.r' 'blandr.draw.r' 'blandr.display.r' 'blandr.display.and.draw.r' 'blandr.display.and.plot.r' 'blandr.method.comparison.r' 'blandr.plot.r' 'blandr.proportional.bias.r'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-26 18:28:02 UTC; deepankardatta
Author: Deepankar Datta [aut, cre]
Maintainer: Deepankar Datta <deepankardatta@nhs.net>
Repository: CRAN
Date/Publication: 2017-07-26 21:48:40 UTC

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Package PracTools updated to version 0.6 with previous version 0.5 dated 2017-07-11

Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>

Diff between PracTools versions 0.5 dated 2017-07-11 and 0.6 dated 2017-07-26

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Package sandwich updated to version 2.4-0 with previous version 2.3-4 dated 2015-09-24

Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.
Author: Achim Zeileis [aut, cre], Thomas Lumley [aut], Susanne Berger [ctb], Nathaniel Graham [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

Diff between sandwich versions 2.3-4 dated 2015-09-24 and 2.4-0 dated 2017-07-26

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Package SpecHelpers updated to version 0.2.7 with previous version 0.2.2 dated 2016-01-26

Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate spectra for use in teaching or testing. 2. Functions to process files created by 'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

Diff between SpecHelpers versions 0.2.2 dated 2016-01-26 and 0.2.7 dated 2017-07-26

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Package ordinalForest updated to version 2.0 with previous version 1.0 dated 2017-04-13

Title: Ordinal Forests: Prediction and Variable Ranking with Ordinal Target Variables
Description: Ordinal forests (OF) are a method for ordinal regression with high-dimensional and low-dimensional data that is able to predict the values of the ordinal target variable for new observations based on a training dataset. Using a (permutation-based) variable importance measure it is moreover possible to rank the covariates with respect to their importances in the prediction of the values of the ordinal target variable. OF will be presented in an upcoming technical report by Hornung et al.. The main functions of the package are: ordfor() (construction of OF) and predict.ordfor() (prediction of the target variable values of new observations).
Author: Roman Hornung
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>

Diff between ordinalForest versions 1.0 dated 2017-04-13 and 2.0 dated 2017-07-26

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New package metaBMA with initial version 0.3.8
Package: metaBMA
Type: Package
Date: 2017-07-26
Title: Bayesian Model Averaging for Random and Fixed Effects Meta-Analysis
Version: 0.3.8
Authors@R: c(person("Daniel W.","Heck",email="heck@uni-mannheim.de",role=c("aut","cre")), person("Quentin F.", "Gronau", email="quentingronau@web.de", role = c("ctb")), person("Eric-Jan", "Wagenmakers", email="ej.wagenmakers@gmail.com", role = c("ctb")))
Maintainer: Daniel W. Heck <heck@uni-mannheim.de>
Description: Computes the posterior model probabilities for four meta-analysis models (null model vs. alternative model assuming either fixed- or random-effects, respectively). These posterior probabilities are used to estimate the overall mean effect size as the weighted average of the mean effect size estimates of the random- and fixed-effect model as proposed by Gronau, Van Erp, Heck, Cesario, Jonas, & Wagenmakers (2017, <doi:10.1080/23743603.2017.1326760>). The user can define a wide range of noninformative or informative priors for the mean effect size and the heterogeneity coefficient. Funding for this research was provided by the Berkeley Initiative for Transparency in the Social Sciences, a program of the Center for Effective Global Action (CEGA), with support from the Laura and John Arnold Foundation.
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.0)
Imports: mvtnorm, logspline, coda, runjags, LaplacesDemon
Suggests: testthat, knitr
VignetteBuilder: knitr
SystemRequirements: JAGS (http://mcmc-jags.sourceforge.net)
URL: https://github.com/danheck/metaBMA
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-26 16:44:33 UTC; Daniel
Author: Daniel W. Heck [aut, cre], Quentin F. Gronau [ctb], Eric-Jan Wagenmakers [ctb]
Repository: CRAN
Date/Publication: 2017-07-26 17:43:28 UTC

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Package ggpval updated to version 0.2.0 with previous version 0.1.0 dated 2017-06-12

Title: Annotate Statistical Tests for 'ggplot2'
Description: Automatically performs desired statistical tests (e.g. wilcox.test(), t.test()) to compare between groups, and adds the resulting p-values to the plot with an annotation bar. Visualizing group differences are frequently performed by boxplots, bar plots, etc. Statistical test results are often needed to be annotated on these plots. This package provides a convenient function that works on 'ggplot2' objects, performs the desired statistical test between groups of interest and annotates the test results on the plot.
Author: Jun Cheng [aut, cre]
Maintainer: Jun Cheng <s6juncheng@gmail.com>

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Package ccRemover updated to version 1.0.2 with previous version 1.0.1 dated 2017-05-18

Title: Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data
Description: Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.
Author: Jun Li [aut, cre], Martin Barron [aut]
Maintainer: Jun Li <jun.li@nd.edu>

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Package BiDAG updated to version 1.0.1 with previous version 1.0.0 dated 2017-07-19

Title: Bayesian Inference for Directed Acyclic Graphs (BiDAG): Software for the Efficient Inference and Sampling of Bayesian Networks
Description: Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
Author: Polina Minkina [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Minkina <polina.minkina@bsse.ethz.ch>

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Package CensMixReg updated to version 3.0 with previous version 1.0 dated 2016-08-08

Title: Censored Linear Mixture Regression Models
Description: Fit censored linear regression models where the random errors follow a finite mixture of Scale Mixture Normal distributions. Fit censored linear models of finite mixture multivariate Student-t and Normal distributions. Fit censored mixture regression models based on scale mixture of normal distributions.
Author: Luis Benites Sanchez[cre, aut], Victor Hugo Lachos[cre, aut], Edgar J. Lopez Moreno[ctb]
Maintainer: Luis Benites Sanchez <lbenitesanchez@gmail.com>

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Package agricolae updated to version 1.2-5 with previous version 1.2-4 dated 2016-06-13

Title: Statistical Procedures for Agricultural Research
Description: Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <fmendiburu@lamolina.edu.pe>

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Package mosaic updated to version 1.0.0 with previous version 0.14.4 dated 2016-07-29

Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan <kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

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 mosaic-1.0.0/mosaic/R/maps2.R                                                                    |    2 
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 mosaic-1.0.0/mosaic/man/MAD_.Rd                                                                  |    1 
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 mosaic-1.0.0/mosaic/man/mid.Rd                                                                   |    1 
 mosaic-1.0.0/mosaic/man/mm.Rd                                                                    |   25 
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 mosaic-1.0.0/mosaic/man/rfun.Rd                                                                  |    2 
 mosaic-1.0.0/mosaic/man/rgeo-internals.Rd                                                        |    3 
 mosaic-1.0.0/mosaic/man/rgeo.Rd                                                                  |    5 
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New package iRF with initial version 2.0.0
Package: iRF
Title: iterative Random Forests
Version: 2.0.0
Date: 2017-07-25
Depends: R (>= 3.1.2),
Imports: AUC, Matrix, data.table, dplyr, Rcpp, methods, foreach, doParallel, RColorBrewer
Suggests: MASS, rgl
LinkingTo: Rcpp
SystemRequirements: C++11
Author: Sumanta Basu and Karl Kumbier (based on source codes from the R packages FSInteract by Hyun Jik Kim and Rajen D. Shah, randomForest by Andy Liaw and Matthew Wiener, and the original Fortran codes by Leo Breiman and Adele Cutler)
Description: Iteratively grows feature weighted random forests and finds high-order feature interactions in a stable fashion.
Maintainer: Karl Kumbier <kkumbier@berkeley.edu>
URL: https://arxiv.org/abs/1706.08457
License: GPL-2
NeedsCompilation: yes
Packaged: 2017-07-25 22:55:38 UTC; karl
Repository: CRAN
Date/Publication: 2017-07-26 04:57:45 UTC

More information about iRF at CRAN
Permanent link

Tue, 25 Jul 2017

Package sweep updated to version 0.2.0 with previous version 0.1.0 dated 2017-07-03

Title: Tidy Tools for Forecasting
Description: Tidies up the forecasting modeling and prediction work flow, extends the 'broom' package with 'sw_tidy', 'sw_glance', 'sw_augment', and 'sw_tidy_decomp' functions for various forecasting models, and enables converting 'forecast' objects to "tidy" data frames with 'sw_sweep'.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between sweep versions 0.1.0 dated 2017-07-03 and 0.2.0 dated 2017-07-25

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More information about sweep at CRAN
Permanent link

Package reticulate updated to version 1.0 with previous version 0.9 dated 2017-06-23

Title: R Interface to Python
Description: R interface to Python modules, classes, and functions. When calling into Python R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types. Compatible with all versions of Python >= 2.7.
Author: JJ Allaire [aut, cre], Kevin Ushey [ctb], RStudio [cph, fnd], Yuan Tang [aut, cph], Dirk Eddelbuettel [ctb, cph], Bryan Lewis [ctb, cph], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between reticulate versions 0.9 dated 2017-06-23 and 1.0 dated 2017-07-25

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More information about reticulate at CRAN
Permanent link

New package concaveman with initial version 1.0.0
Package: concaveman
Type: Package
Title: A Very Fast 2D Concave Hull Algorithm
Version: 1.0.0
Authors@R: c( person("Joël", "Gombin", email="joel.gombin@gmail.com", role = c("cre", "aut")), person("Ramnath", "Vaidyanathan", role = "aut"), person("Vladimir", "Agafonkin", role = "aut"), person("Mapbox", role = "cph") )
Description: The concaveman function ports the 'concaveman' (<https://github.com/mapbox/concaveman>) library from 'mapbox'. It computes the concave polygon(s) for one or several set of points.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: V8, sf, magrittr, jsonlite, methods, dplyr
RoxygenNote: 6.0.1
Suggests: testthat, sp
URL: http://www.github.com/joelgombin/concaveman
BugReports: http://www.github.com/joelgombin/concaveman/issues
SystemRequirements: GDAL (>= 2.0.0), GEOS (>= 3.3.0), PROJ.4 (>= 4.8.0)
NeedsCompilation: no
Packaged: 2017-07-25 21:57:11 UTC; joel
Author: Joël Gombin [cre, aut], Ramnath Vaidyanathan [aut], Vladimir Agafonkin [aut], Mapbox [cph]
Maintainer: Joël Gombin <joel.gombin@gmail.com>
Repository: CRAN
Date/Publication: 2017-07-25 22:37:09 UTC

More information about concaveman at CRAN
Permanent link

Package VGAM updated to version 1.0-4 with previous version 1.0-3 dated 2017-01-11

Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of statistical regression models. At the heart of it are the vector generalized linear and additive model (VGLM/VGAM) classes, and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and VGAM package. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

Diff between VGAM versions 1.0-3 dated 2017-01-11 and 1.0-4 dated 2017-07-25

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New package timetk with initial version 0.1.0
Package: timetk
Type: Package
Title: A Tool Kit for Working with Time Series in R
Version: 0.1.0
Date: 2017-07-25
Authors@R: c( person("Matt", "Dancho", email = "mdancho@business-science.io", role = c("aut", "cre")), person("Davis", "Vaughan", email = "dvaughan@business-science.io", role = c("aut")) )
Description: Get the time series index, signature, and summary from time series objects and time-based tibbles. Create future time series based on properties of existing time series index. Coerce between time-based tibbles ('tbl') and 'xts', 'zoo', and 'ts'.
URL: https://github.com/business-science/timetk
BugReports: https://github.com/business-science/timetk/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: devtools (>= 1.12.0), dplyr (>= 0.7.0), forecast (>= 0.8.0), lazyeval (>= 0.2.0), lubridate (>= 1.6.0), padr (>= 0.3.0), purrr (>= 0.2.2), readr (>= 1.0.0), stringi (>= 1.1.5), tibble (>= 1.2), tidyr (>= 0.6.1), xts (>= 0.9-7), zoo (>= 1.7-14)
Suggests: broom, forcats, knitr, rmarkdown, robets, scales, stringr, testthat, tidyverse, tidyquant
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-07-25 16:53:08 UTC; mdancho
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Repository: CRAN
Date/Publication: 2017-07-25 21:43:26 UTC

More information about timetk at CRAN
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Package RxnSim updated to version 1.0.3 with previous version 1.0.2 dated 2017-06-20

Title: Functions to Compute Chemical Reaction Similarity
Description: Methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages 'rCDK' and 'fingerprint' for cheminformatics functionality.
Author: Varun Giri [aut, cre]
Maintainer: Varun Giri <varungiri@gmail.com>

Diff between RxnSim versions 1.0.2 dated 2017-06-20 and 1.0.3 dated 2017-07-25

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Package rtypeform updated to version 0.3.1 with previous version 0.3.0 dated 2017-05-03

Title: Interface to 'typeform' Results
Description: An R interface to the 'typeform' <https://typeform.com> application program interface. Also provides functions for downloading your results.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>

Diff between rtypeform versions 0.3.0 dated 2017-05-03 and 0.3.1 dated 2017-07-25

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New package MiRKAT with initial version 1.0
Package: MiRKAT
Version: 1.0
Date: 2017-07-25
Title: Microbiome Regression-Based Kernel Association Test
Authors@R: c(person("Haotian", "Zheng", role = c("aut"), email = "ht-zh14@mails.tsighua.edu.cn"), person("Xiang", "Zhan", role = "aut"), person("Anna", "Plantinga", role = "aut"), person("Michael", "Wu", role = "aut"), person("Ni", "Zhao", role = c("aut", "cre"), email = "nzhao10@jhu.edu"))
Author: Haotian Zheng [aut], Xiang Zhan [aut], Anna Plantinga [aut], Michael Wu [aut], Ni Zhao [aut, cre]
Maintainer: Ni Zhao <nzhao10@jhu.edu>
Depends: R (>= 2.13.0), survival, PearsonDS, GUniFrac, MASS
Description: Test for overall association between microbiome composition data with a continuous or dichotomous outcome via phylogenetic kernels. The phenotype can be univariate continuous or binary phenotypes (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). For all these effect, the microbiome community effect was modeled nonparametrically through a kernel function, which can incorporate the phylogenetic tree information.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2017-07-25 20:54:07 UTC; dell
Repository: CRAN
Date/Publication: 2017-07-25 21:52:56 UTC

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Package gamm4 updated to version 0.2-5 with previous version 0.2-4 dated 2016-09-17

Title: Generalized Additive Mixed Models using 'mgcv' and 'lme4'
Description: Estimate generalized additive mixed models via a version of function gamm() from 'mgcv', using 'lme4' for estimation.
Author: Simon Wood, Fabian Scheipl
Maintainer: Simon Wood <simon.wood@r-project.org>

Diff between gamm4 versions 0.2-4 dated 2016-09-17 and 0.2-5 dated 2017-07-25

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New package bayeslongitudinal with initial version 0.1.0
Package: bayeslongitudinal
Type: Package
Title: Adjust Longitudinal Regression Models Using Bayesian Methodology
Version: 0.1.0
Date: 2017-07-18
Author: Edwin Javier Castillo Carreño, Edilberto Cepeda Cuervo
Maintainer: Edwin Javier Castillo Carreño <edjcastilloca@unal.edu.co>
Description: Adjusts longitudinal regression models using Bayesian methodology for covariance structures of composite symmetry (SC), autoregressive ones of order 1 AR (1) and autoregressive moving average of order (1,1) ARMA (1,1).
License: GPL (>= 2)
Depends: R(>= 3.1.0), LearnBayes, mvtnorm, MASS
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-18 21:21:17 UTC; edwin
Repository: CRAN
Date/Publication: 2017-07-25 21:13:13 UTC

More information about bayeslongitudinal at CRAN
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Package timekit (with last version 0.3.1) was removed from CRAN

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

2017-06-28 0.3.1
2017-05-16 0.3.0
2017-04-30 0.2.0
2017-04-19 0.1.0

Permanent link
Package sequoia updated to version 0.9.3 with previous version 0.9.2 dated 2017-07-17

Title: Pedigree Inference from SNPs
Description: Fast multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See citation('sequoia') for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>

Diff between sequoia versions 0.9.2 dated 2017-07-17 and 0.9.3 dated 2017-07-25

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Package QTLRel updated to version 0.2-17 with previous version 0.2-16 dated 2017-07-20

Title: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>

Diff between QTLRel versions 0.2-16 dated 2017-07-20 and 0.2-17 dated 2017-07-25

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Package qtlmt updated to version 0.1-6 with previous version 0.1-5 dated 2017-07-20

Title: Tools for Mapping Multiple Complex Traits
Description: Provides tools for joint analysis of multiple traits in a backcross (BC) or recombinant inbred lines (RIL) population. It can be used to select an optimal subset of traits for multiple-trait mapping, analyze multiple traits via the SURE model, which can associate different QTL with different traits, and perform multiple-trait composite multiple-interval mapping.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>

Diff between qtlmt versions 0.1-5 dated 2017-07-20 and 0.1-6 dated 2017-07-25

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Package gambin updated to version 2.1.1 with previous version 1.4 dated 2016-06-22

Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data. 'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre], Michael Krabbe Borregaard [aut], Karl Ugland [aut], Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>

Diff between gambin versions 1.4 dated 2016-06-22 and 2.1.1 dated 2017-07-25

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Package netCoin updated to version 0.2.6 with previous version 0.2.5 dated 2017-03-31

Title: Interactive Networks with R
Description: Create interactive networked coincidences. It joins the data analysis power of R to study coincidences and the visualization libraries of JavaScript in one package.
Author: Modesto Escobar <modesto@usal.es>, Carlos Prieto <cprietos@usal.es>, David Barrios <metal@usal.es>, Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>

Diff between netCoin versions 0.2.5 dated 2017-03-31 and 0.2.6 dated 2017-07-25

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New package qqplotr with initial version 0.0.1
Package: qqplotr
Type: Package
Version: 0.0.1
Title: Quantile-Quantile Plot Extensions for 'ggplot2'
Description: Extensions of 'ggplot2' Q-Q plot functionalities.
Authors@R: c(person("Alexandre", "Almeida", email = "almeida.xan@gmail.com", role = c("aut", "cre")), person("Adam", "Loy", email = "loyad01@gmail.com", role = c("aut")), person("Heike", "Hofmann", role = "aut"))
URL: https://github.com/aloy/qqplotr
BugReports: https://github.com/aloy/qqplotr/issues
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Collate: 'stat_qq_point.R' 'stat_qq_line.R' 'stat_qq_band.R'
Depends: ggplot2
Imports: dplyr, robustbase, stats4
NeedsCompilation: no
Packaged: 2017-07-22 19:46:03 UTC; almeida
Author: Alexandre Almeida [aut, cre], Adam Loy [aut], Heike Hofmann [aut]
Maintainer: Alexandre Almeida <almeida.xan@gmail.com>
Repository: CRAN
Date/Publication: 2017-07-25 17:34:47 UTC

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Package glmm updated to version 1.2 with previous version 1.1.1 dated 2016-08-17

Title: Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson <christina@umn.edu>

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Package PowerNormal updated to version 1.2.0 with previous version 1.1.0 dated 2017-06-25

Title: Power Normal Distribution
Description: Miscellaneous functions for a descriptive analysis and initial Bayesian and classical inference for the power parameter of the the Power Normal (PN) distribution. This miscellaneous will be extend for more distributions into the power family and the three-parameter model.
Author: Gualberto Segundo Agamez Montalvo, Marcia D'Elia Branco
Maintainer: Gualberto Segundo Agamez Montalvo <gsagamez@gmail.com>

Diff between PowerNormal versions 1.1.0 dated 2017-06-25 and 1.2.0 dated 2017-07-25

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Package aniDom updated to version 0.1.2 with previous version 0.1.1 dated 2017-04-28

Title: Inferring Dominance Hierarchies and Estimating Uncertainty
Description: Provides: (1) Tools to infer dominance hierarchies based on calculating Elo scores, but with custom functions to improve estimates in animals with relatively stable dominance ranks. (2) Tools to plot the shape of the dominance hierarchy and estimate the uncertainty of a given data set.
Author: Damien R. Farine and Alfredo Sanchez-Tojar
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>

Diff between aniDom versions 0.1.1 dated 2017-04-28 and 0.1.2 dated 2017-07-25

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Package seqICP updated to version 1.1 with previous version 1.0 dated 2017-06-27

Title: Sequential Invariant Causal Prediction
Description: Contains an implementation of invariant causal prediction for sequential data. The main function in the package is 'seqICP', which performs linear sequential invariant causal prediction and has guaranteed type I error control. For non-linear dependencies the package also contains a non-linear method 'seqICPnl', which allows to input any regression procedure and performs tests based on a permutation approach that is only approximately correct. In order to test whether an individual set S is invariant the package contains the subroutines 'seqICP.s' and 'seqICPnl.s' corresponding to the respective main methods.
Author: Niklas Pfister and Jonas Peters
Maintainer: Niklas Pfister <pfister@stat.math.ethz.ch>

Diff between seqICP versions 1.0 dated 2017-06-27 and 1.1 dated 2017-07-25

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Package WhatIf updated to version 1.5-9 with previous version 1.5-8 dated 2017-03-21

Title: Evaluate Counterfactuals
Description: Inferences about counterfactuals are essential for prediction, answering what if questions, and estimating causal effects. However, when the counterfactuals posed are too far from the data at hand, conclusions drawn from well-specified statistical analyses become based largely on speculation hidden in convenient modeling assumptions that few would be willing to defend. Unfortunately, standard statistical approaches assume the veracity of the model rather than revealing the degree of model-dependence, which makes this problem hard to detect. WhatIf offers easy-to-apply methods to evaluate counterfactuals that do not require sensitivity testing over specified classes of models. If an analysis fails the tests offered here, then we know that substantive inferences will be sensitive to at least some modeling choices that are not based on empirical evidence, no matter what method of inference one chooses to use. WhatIf implements the methods for evaluating counterfactuals discussed in Gary King and Langche Zeng, 2006, "The Dangers of Extreme Counterfactuals," Political Analysis 14 (2) <DOI:10.1093/pan/mpj004>; and Gary King and Langche Zeng, 2007, "When Can History Be Our Guide? The Pitfalls of Counterfactual Inference," International Studies Quarterly 51 (March) <DOI:10.1111/j.1468-2478.2007.00445.x>.
Author: Christopher Gandrud [aut, cre], Gary King [aut], Ben Sabath [ctb], Heather Stoll [aut], Langche Zeng [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>

Diff between WhatIf versions 1.5-8 dated 2017-03-21 and 1.5-9 dated 2017-07-25

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Package ggseqlogo updated to version 0.1 with previous version 0.0.1 dated 2017-06-13

Title: A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos
Description: The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.
Author: Omar Wagih
Maintainer: Omar Wagih <wagih@ebi.ac.uk>

Diff between ggseqlogo versions 0.0.1 dated 2017-06-13 and 0.1 dated 2017-07-25

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New package MRTSampleSize with initial version 0.1.0
Package: MRTSampleSize
Type: Package
Title: A Sample Size Calculator for Micro-Randomized Trials
Version: 0.1.0
Authors@R: c( person("Liying","Huang", email = "lxh37@psu.edu", role = c("aut","cre")), person("Nicholas J.","Seewald", email = "nseewald@umich.edu", role = "aut"), person("Peng","Liao", email = "pengliao@umich.edu", role ="aut"), person("Ji","Sun", email = "sunji@umich.edu", role ="aut"))
Depends: R (>= 2.15.0)
Copyright: The Pennsylvania State University
Description: Provide a sample size calculator for micro-randomized trials (MRTs) based on methodology developed in Sample Size Calculations for Micro-randomized Trials in mHealth by Liao et al. (2016) <DOI:10.1002/sim.6847>.
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-07-21 13:15:14 UTC; admin_lxh37
Author: Liying Huang [aut, cre], Nicholas J. Seewald [aut], Peng Liao [aut], Ji Sun [aut]
Maintainer: Liying Huang <lxh37@psu.edu>
Repository: CRAN
Date/Publication: 2017-07-25 11:06:21 UTC

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Package rcompanion updated to version 1.9.1 with previous version 1.5.7 dated 2017-06-23

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of Extension Education Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

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Package tbl2xts updated to version 0.1.1 with previous version 0.1.0 dated 2017-06-23

Title: Convert Tibbles or Data Frames to Xts Easily
Description: Facilitate the movement between data frames to 'xts'. Particularly useful when moving from 'tidyverse' to the widely used 'xts' package, which is the input format of choice to various other packages. It also allows the user to use a 'spread_by' argument for a character column 'xts' conversion.
Author: Nico Katzke
Maintainer: Nico Katzke <nfkatzke@gmail.com>

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Package Directional updated to version 2.8 with previous version 2.7 dated 2017-05-17

Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Directional versions 2.7 dated 2017-05-17 and 2.8 dated 2017-07-25

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New package treeDA with initial version 0.0.2
Package: treeDA
Title: Tree-Based Discriminant Analysis
Version: 0.0.2
Authors@R: person("Julia", "Fukuyama", email = "julia.fukuyama@gmail.com", role = c("aut", "cre"))
Description: Performs sparse discriminant analysis on a combination of node and leaf predictors when the predictor variables are structured according to a tree.
Depends: R (>= 3.4.1)
Imports: sparseLDA (>= 0.1.9), Matrix (>= 1.2.10), mvtnorm (>= 1.0.6), reshape2 (>= 1.4.2), gtable (>= 0.2.0), grid (>= 3.4.1), phyloseq (>= 1.20.0), ggplot2 (>= 2.2.1), stats (>= 3.4.1)
Suggests: adaptiveGPCA (>= 0.1), knitr (>= 1.16)
VignetteBuilder: knitr
License: GPL-2
URL: https://github.com/jfukuyama/treeda
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-24 21:59:20 UTC; juliefukuyama
Author: Julia Fukuyama [aut, cre]
Maintainer: Julia Fukuyama <julia.fukuyama@gmail.com>
Repository: CRAN
Date/Publication: 2017-07-25 08:30:30 UTC

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Package TreatmentSelection updated to version 2.1.0 with previous version 2.0.3 dated 2017-02-09

Title: Evaluate Treatment Selection Biomarkers
Description: A suite of descriptive and inferential methods designed to evaluate one or more biomarkers for their ability to guide patient treatment recommendations. Package includes functions to assess the calibration of risk models; and plot, evaluate, and compare markers.
Author: Marshall Brown and Holly Janes
Maintainer: Marshall Brown <mdbrown@fhcrc.org>

Diff between TreatmentSelection versions 2.0.3 dated 2017-02-09 and 2.1.0 dated 2017-07-25

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Package sidrar updated to version 0.2.4 with previous version 0.2.1 dated 2017-06-29

Title: An Interface to IBGE's SIDRA API
Description: Allows the user to connect with IBGE's (Instituto Brasileiro de Geografia e Estatistica, see <http://www.ibge.gov.br/> for more information) SIDRA API in a flexible way. SIDRA is the acronym to "Sistema IBGE de Recuperacao Automatica" and is the system where IBGE turns available aggregate data from their researches.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>

Diff between sidrar versions 0.2.1 dated 2017-06-29 and 0.2.4 dated 2017-07-25

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New package pulver with initial version 0.1.0
Package: pulver
Title: Parallel Ultra-Rapid p-Value Computation for Linear Regression Interaction Terms
Version: 0.1.0
Authors@R: person("Sophie", "Molnos", email = "somolnos@gmail.com", role = c("aut", "cre"))
Maintainer: Sophie Molnos <somolnos@gmail.com>
Description: Computes p-values for the interaction term in a very large number of linear regression models.
Depends: R (>= 3.3.0)
License: GPL (>= 2)
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, DatABEL, parallel, methods
Suggests: testthat, knitr, rmarkdown, devtools
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-07-25 07:37:16 UTC; sophie.molnos
Author: Sophie Molnos [aut, cre]
Repository: CRAN
Date/Publication: 2017-07-25 08:26:31 UTC

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New package PSIMEX with initial version 1.0
Package: PSIMEX
Type: Package
Title: SIMEX Algorithm on Pedigree Structures
Version: 1.0
Depends: MCMCglmm, plotrix, pedigree, knitr
VignetteBuilder: knitr
Date: 2017-07-23
Author: Erica Ponzi
Maintainer: Erica Ponzi <erica.ponzi@uzh.ch>
Description: Generalization of the SIMEX algorithm from Cook & Stefanski (1994) <doi:10.2307/2290994> for the calculation of inbreeding depression or heritability on pedigree structures affected by missing or misassigned paternities. It simulates errors and tracks the behavior of the estimate as a function of the error proportion. It extrapolates back a true value corresponding to the null error rate.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2017-07-25 07:13:48 UTC; ericapo
Repository: CRAN
Date/Publication: 2017-07-25 08:23:59 UTC

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Package datasus updated to version 0.4.0 with previous version 0.1.0 dated 2017-06-12

Title: An Interface to DATASUS System
Description: It allows the user to retrieve the data from the systems of DATASUS (SUS IT department related to the Brazilian Ministry of Health, see <http://datasus.saude.gov.br/informacoes-de-saude/tabnet/> for more information) much in the same way that is done in the online portal. For now the package allows access to the SINASC and SIM's (ICD-10) systems, that is, the 'Estatísticas Vitais'.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>

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New package curstatCI with initial version 0.1.0
Package: curstatCI
Type: Package
Title: Confidence Intervals for the Current Status Model
Version: 0.1.0
Authors@R: c( person("Piet", "Groeneboom", email = "P.Groeneboom@tudelft.nl",role = "aut"), person("Kim", "Hendrickx", email = "kim.hendrickx@uhasselt.be",role = "cre"))
Description: Computes the maximum likelihood estimator, the smoothed maximum likelihood estimator and pointwise bootstrap confidence intervals for the distribution function under current status data. Groeneboom and Hendrickx (2017) <arXiv:1701.07359>.
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp
Depends: R (>= 2.10)
RoxygenNote: 6.0.1
URL: https://github.com/kimhendrickx/curstatCI
BugReports: https://github.com/kimhendrickx/curstatCI/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-07-25 08:41:11 UTC; lucp8442
Author: Piet Groeneboom [aut], Kim Hendrickx [cre]
Maintainer: Kim Hendrickx <kim.hendrickx@uhasselt.be>
Repository: CRAN
Date/Publication: 2017-07-25 08:50:19 UTC

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Package CerioliOutlierDetection updated to version 1.1.9 with previous version 1.1.5 dated 2016-07-08

Title: Outlier Detection Using the Iterated RMCD Method of Cerioli (2010)
Description: Implements the iterated RMCD method of Cerioli (2010) for multivariate outlier detection via robust Mahalanobis distances. Also provides the finite-sample RMCD method discussed in the paper, as well as the methods provided in Hardin and Rocke (2005) <doi:10.1198/106186005X77685> and Green and Martin (2017).
Author: Christopher G. Green [aut, cre], R. Doug Martin [ths]
Maintainer: Christopher G. Green <christopher.g.green@gmail.com>

Diff between CerioliOutlierDetection versions 1.1.5 dated 2016-07-08 and 1.1.9 dated 2017-07-25

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Package BioInstaller updated to version 0.2.0 with previous version 0.1.2 dated 2017-06-23

Title: Lightweight Biology Software Installer
Description: Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

Diff between BioInstaller versions 0.1.2 dated 2017-06-23 and 0.2.0 dated 2017-07-25

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Mon, 24 Jul 2017

New package ThermIndex with initial version 0.1.0
Package: ThermIndex
Type: Package
Title: Calculate Thermal Indexes
Version: 0.1.0
Author: Francisco Jablinski Castelhano/Laboclima - Universidade Federal do Paraná
Maintainer: Francisco Jablinski Castelhano <fjcastelhano@gmail.com>
Description: Calculates several thermal comfort indexes using temperature, wind speed and relative humidity values, calculating indexes such as Humidex, windchill, Discomfort Index and others.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-07-24 19:49:49 UTC; Chico
Repository: CRAN
Date/Publication: 2017-07-24 22:08:45 UTC

More information about ThermIndex at CRAN
Permanent link

Package SKAT updated to version 1.3.2 with previous version 1.3.0 dated 2017-05-18

Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>

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Package shinyWidgets updated to version 0.3.2 with previous version 0.3.0 dated 2017-06-11

Title: Custom Inputs Widgets for Shiny
Description: Some custom inputs widgets to use in Shiny applications, like a toggle switch to replace checkboxes. And other components to pimp your apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], Silvio Moreto [ctb, cph] (bootstrap-select), Ana Carolina [ctb, cph] (bootstrap-select), caseyjhol [ctb, cph] (bootstrap-select), Matt Bryson [ctb, cph] (bootstrap-select), t0xicCode [ctb, cph] (bootstrap-select), Mattia Larentis [ctb, cph] (Bootstrap Switch), Emanuele Marchi [ctb, cph] (Bootstrap Switch), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Flatlogic [cph] (Awesome Bootstrap Checkbox), mouse0270 [ctb, cph] (Material Design Switch), Tristan Edwards [ctb, cph] (SweetAlert), Fabian Lindfors [ctb, cph] (multi.js), Daniel Eden [ctb, cph] (animate.css), Ganapati V S [ctb, cph] (bttn.css)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package plumber updated to version 0.4.2 with previous version 0.3.2 dated 2017-05-22

Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.
Author: Trestle Technology, LLC [aut], Jeff Allen [cre], Frans van Dunné [ctb], SmartBear Software [ctb, cph] (swagger-ui)
Maintainer: Jeff Allen <cran@trestletech.com>

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More information about plumber at CRAN
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Package joineR updated to version 1.2.1 with previous version 1.2.0 dated 2017-05-19

Title: Joint Modelling of Repeated Measurements and Time-to-Event Data
Description: Analysis of repeated measurements and time-to-event data via random effects joint models. Fits the joint models proposed by Henderson and colleagues <doi:10.1093/biostatistics/1.4.465> (single event time) and by Williamson and colleagues (2008) <doi:10.1002/sim.3451> (competing risks events time) to a single continuous repeated measure. The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-varying covariates. The longitudinal outcome is modelled using a linear mixed effects model. The association is captured by a latent Gaussian process. The model is estimated using am Expectation Maximization algorithm. Some plotting functions and the variogram are also included. This project is funded by the Medical Research Council (Grant numbers G0400615 and MR/M013227/1).
Author: Pete Philipson [aut], Ines Sousa [aut], Peter J. Diggle [aut], Paula Williamson [aut], Ruwanthi Kolamunnage-Dona [aut], Robin Henderson [aut], Graeme L. Hickey [aut, cre], Maria Sudell [ctb]
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>

Diff between joineR versions 1.2.0 dated 2017-05-19 and 1.2.1 dated 2017-07-24

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Package HTSSIP updated to version 1.2.0 with previous version 1.1.1 dated 2017-05-23

Title: High Throughput Sequencing of Stable Isotope Probing Data Analysis
Description: Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).
Author: Nicholas Youngblut [aut, cre], Samuel Barnett [ctb]
Maintainer: Nicholas Youngblut <nyoungb2@gmail.com>

Diff between HTSSIP versions 1.1.1 dated 2017-05-23 and 1.2.0 dated 2017-07-24

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Package hIRT updated to version 0.1.1 with previous version 0.1.0 dated 2017-07-23

Title: Hierarchical Item Response Theory Models
Description: Implementation of a class of hierarchical item response theory (IRT) models where both the mean and the variance of latent preferences (ability parameters) can depend on observed covariates. The current implementation includes both the two-parameter latent trait model and the graded response model. Both are fitted via the Expectation-Maximization (EM) algorithm. Asymptotic standard errors are derived from the observed information matrix.
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>

Diff between hIRT versions 0.1.0 dated 2017-07-23 and 0.1.1 dated 2017-07-24

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