CRAN (and crantastic) updates this week New packages ------------
* adaptDA (1.0) Maintainer: Charles Bouveyron Author(s): Charles Bouveyron License: GPL-2 http://crantastic.org/packages/adaptDA The adaptive mixture discriminant analysis (AMDA) allows to adapt a model-based classifier to the situation where a class represented in the test set may have not been encountered earlier in the learning phase. * aRxiv (0.5.2) Maintainer: Karl W Broman Author(s): Karthik Ram [aut], Karl Broman [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/aRxiv An interface to the API for arXiv, a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics. * audited (1.9) Maintainer: Tim Bergsma Author(s): Tim Bergsma License: GPL http://crantastic.org/packages/audited Classifies a data.frame such that row deletions and additions are tracked. A mechanism exists to give formal names to the row subsets that are coming or going. These names are used to populate a directed graph giving an account of all the transactions contributing to the state of the data.frame. The generic as.audited() has a method for keyed data.frames that creates an audited data.frame. Methods exist that track row count changes for the generics: Ops, !, ^, |, [, subset, head, tail, unique, cast, melt, aggregate, and merge. audit() extracts the transaction table from the audited object, while write.audit() and read.audit() control exchange with the file system. An audit method for as.igraph() creates a graph object that can be displayed with the corresponding plot method. Use options(audit= ) to provide an extra level of classification. Use options(artifact=TRUE) and as.xlsx() to save dropped records to file. * BEANSP (1.0) Maintainer: Yiqun Yang Author(s): Chong He, Yiqun Yang, Jing Cao License: GPL-2 http://crantastic.org/packages/BEANSP Computing age specific nest survival rates based on a Bayesian hierarchical model. This package can handle unknown nest age, irregular visiting schedule and nest-specific covariates. * binequality (0.6.1) Maintainer: Samuel V. Scarpino Author(s): Samuel V. Scarpino, Paul von Hippel, and Igor Holas License: GPL (>= 3.0) http://crantastic.org/packages/binequality Methods for model selection, model averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation, etc, on binned income data where the topmost bin is right-censored. We provide both a non-parametric method, termed the bounded midpoint estimator (BME), which assigns cases to their bin midpoints; except for the censored bins, where cases are assigned to an income estimated by fitting a Pareto distribution. Because the usual Pareto estimate can be inaccurate or undefined, especially in small samples, we implement a bounded Pareto estimate that yields much better results. We also provide a parametric approach, which fits distributions from the generalized beta (GB) family. Because some GB distributions can have poor fit or undefined estimates, we fit 10 GB-family distributions and use multimodel inference to obtain definite estimates from the best-fitting distributions. We also provide binned income data from all United States of America school districts, counties, and states. * BOIN (1.0) Maintainer: Ying Yuan Author(s): Ying Yuan and Suyu Liu License: GPL-2 http://crantastic.org/packages/BOIN The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields average performance comparable to the continual reassessment method (CRM, one of the best model-based design) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses. * confidence (1.0-0) Maintainer: Dennis Walvoort Author(s): Willem M. G. M. van Loon [aut, cph], Dennis J. J. Walvoort [aut, cre] License: GPL (>= 3) http://crantastic.org/packages/confidence Functions for estimating and reporting multiyear averages and corresponding confidence intervals and distributions. A potential use case is reporting the chemical and ecological status of surface waters according to the European Water Framework Directive. * GlobalOptions (0.0.1) Maintainer: Zuguang Gu Author(s): Zuguang Gu License: GPL (>= 2) http://crantastic.org/packages/GlobalOptions Generate functions to get or set global options * hot.deck (1.0) Maintainer: Dave Armstrong Author(s): Skyler Cranmer, Jeff Gill, Natalie Jackson, Andreas Murr, Dave Armstrong License: GPL (>= 2) http://crantastic.org/packages/hot-deck Performs multiple hot-deck imputation of categorical and continuous variables in a data frame. * iki.dataclim (1.0) Maintainer: Boris Orlowsky Author(s): Boris Orlowsky License: GPL-3 http://crantastic.org/packages/iki-dataclim The package offers an S4 infrastructure to store climatological station data of various temporal aggregation scales. In-built quality control and homogeneity tests follow the methodology from the European Climate Assessment & Dataset project. Wrappers for climate indices defined by the Expert Team on Climate Change Detection and Indices (ETCCDI), a quick summary of important climate statistics and climate diagram plots provide a fast overview of climatological characteristics of the station. * kselection (0.1.0) Maintainer: Daniel Rodriguez Perez Author(s): Daniel Rodriguez Perez License: GPL-3 http://crantastic.org/packages/kselection Selection of k in k-means clustering based on Pham et al. paper ``Selection of k in k-means clustering'' * m4fe (0.1) Maintainer: Nathan Esau Author(s): Nathan Esau <ne...@sfu.ca> License: GPL-2 http://crantastic.org/packages/m4fe Provides binomial tree models for European, American and Asian Options as well as Interest Rates. Monte Carlo Simulation and Methods for Solving Differential Equations are also included. * MatchingFrontier (0.3.17) Maintainer: Christopher Lucas Author(s): Gary King, Christopher Lucas, and Richard Nielsen License: GPL-3 http://crantastic.org/packages/MatchingFrontier MatchingFrontier returns the subset of the data with the minimum imbalance for every possible subset size (N - 1, N - 2, ...), down to the data set with the minimum possible imbalance. The package also includes tools for the estimation of causal effects for each subset size, as well as functions for visualization and data export. * MST (1.0) Maintainer: Peter Calhoun Author(s): Xiaogang Su, Peter Calhoun, and Juanjuan Fan License: GPL-2 http://crantastic.org/packages/MST Constructs trees for multivariate survival data using marginal and frailty models * multipleNCC (1.0) Maintainer: Nathalie C. Stoer Author(s): Nathalie C. Stoer, Sven Ove Samuelsen License: GPL-2 http://crantastic.org/packages/multipleNCC This package fit Cox proportional hazard models with a weighted partial likelihood. It handles one or multiple endpoints, additional matching and makes it possible to reuse controls for other endpoints. * nat.nblast (1.5) Maintainer: James Manton Author(s): Greg Jefferis and James Manton License: GPL-3 http://crantastic.org/packages/nat-nblast Extends package nat (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions. * nat.templatebrains (0.4.1) Maintainer: James Manton Author(s): James Manton and Greg Jefferis License: GPL-3 http://crantastic.org/packages/nat-templatebrains Extends package nat (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains. * nlWaldTest (1.0.1) Maintainer: Oleh Komashko Author(s): Oleh Komashko License: GPL (>= 2) http://crantastic.org/packages/nlWaldTest Nonlinear restrictions Wald Test for regression parameters using delta-method * opentraj (1.0) Maintainer: Thalles Silva Author(s): Thalles Santos Silva License: GPL-2 http://crantastic.org/packages/opentraj opentraj uses the Hybrid Single Particle Lagrangian Integrated Trajectory Model (HYSPLIT) for computing simple air parcel trajectories. The functions in this package allow users to run HYSPLIT for trajectory calculations, as well as get its results, directly from R without using any GUI interface. * polidata (0.1.0) Maintainer: Eunjeong Park Author(s): Eunjeong Park [aut, cre], Jong Hee Park [aut] License: MIT + file LICENSE http://crantastic.org/packages/polidata This package provides easy access to various political data APIs directly from R. For example, you can access Google Civic Information API (https://developers.google.com/civic-information/) or Sunlight Congress API (https://sunlightlabs.github.io/congress/) for US Congress data, and POPONG API (http://data.popong.com/) for South Korea National Assembly data. * powerr (0.1-3) Maintainer: Jingfan Sun Author(s): Jingfan Sun [aut, cre] License: GPL (>= 2) http://crantastic.org/packages/powerr 'powerr' is used for electric power system analysis and control, including basic power flow analysis and CASCADE analysis. Other features will be updated soon. * propOverlap (1.0) Maintainer: Osama Mahmoud Author(s): Osama Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad Khan, Berthold Lausen License: GPL (>= 2) http://crantastic.org/packages/propOverlap A package for selecting the most relevant features (genes) in the high-dimensional binary classification problems. The discriminative features are identified using analyzing the overlap between the expression values across both classes. The package includes functions for measuring the proportional overlapping score for each gene avoiding the outliers effect. The used measure for the overlap is the one defined in the "Proportional Overlapping Score (POS)" technique for feature selection. A gene mask which represents a gene's classification power can also be produced for each gene (feature). The set size of the selected genes might be set by the user. The minimum set of genes that correctly classify the maximum number of the given tissue samples (observations) can be also produced. * qdapRegex (0.1.1) Maintainer: Tyler Rinker Author(s): Jason Gray [ctb], Tyler Rinker [aut, cre] License: GPL-2 http://crantastic.org/packages/qdapRegex A collection of regex tools associated with the qdap package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, person tags, phone numbers, times, and zip codes. * qgtools (1.0) Maintainer: Jixiang Wu Author(s): Jixiang Wu (South Dakota State University), Johnie N. Jenkins and Jack C. McCarty (USDA-ARS) License: GPL-2 http://crantastic.org/packages/qgtools Two linear mixed model approaches: REML(restricted maximum likelihood) and MINQUE (minimum norm quadratic unbiased estimation) approaches and several resampling techniques are integrated for various quantitative genetics analyses. With these two types of approaches, various unbalanced data structures, missing data, and any irregular genetic mating designs can be analyzed and statistically tested. This package also offers fast computations for many large data sets. Other functions will be added to this R tool in the future. * redcapAPI (1.0) Maintainer: Benjamin Nutter Author(s): Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with contributions from Jeremy Stephens, and Will Beasley License: GPL-2 http://crantastic.org/packages/redcapAPI Access data stored in REDCap databases using the Application Programming Interface (API). REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The redcapAPI package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary. * REDCapR (0.4-28) Maintainer: Will Beasley Author(s): Will Beasley [aut, cre], David Bard [ctb], Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] License: GPL-3 http://crantastic.org/packages/REDCapR Encapsulates functions to streamline calls from R * rmarkdown (0.3.3) Maintainer: JJ Allaire Author(s): JJ Allaire, Jonathan McPherson, Yihui Xie, Hadley Wickham, Joe Cheng, Jeff Allen License: GPL-3 http://crantastic.org/packages/rmarkdown Convert R Markdown documents into a variety of formats including HTML, MS Word, PDF, and Beamer. * RMOA (1.0) Maintainer: Jan Wijffels Author(s): Jan Wijffels [aut, cre], BNOSAC [cph] License: GPL-3 http://crantastic.org/packages/RMOA Connect R with MOA (Massive Online Analysis - http://moa.cms.waikato.ac.nz) to build classification models and regression models on streaming data or out-of-RAM data * RMOAjars (1.0) Maintainer: Jan Wijffels Author(s): See file AUTHORS License: GPL-3 http://crantastic.org/packages/RMOAjars External jars required for package RMOA. RMOA is a framework to build data stream models on top of MOA (Massive Online Analysis - http://moa.cms.waikato.ac.nz) * RRreg (0.1.3) Maintainer: Daniel W. Heck Author(s): Daniel W. Heck [aut, cre], Morten Moshagen [aut] License: GPL-2 http://crantastic.org/packages/RRreg RRreg provides univariate and multivariate methods to analyze randomized response (RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A survey technique for eliminating evasive answer bias. Journal of the American Statistical Association, 60, 63â69). Besides univariate estimates of true proportions, RR variables can be used for correlations, as dependent variable in a logistic regression and as predictors in a linear regression. For simulation and bootstrap purposes, RR data can be generated according to several models. * smoother (1.0.0.0) Maintainer: Nicholas Hamilton Author(s): Nicholas Hamilton License: GPL-2 http://crantastic.org/packages/smoother A port of the matlab gaussian window smoothing function * SOR (0.22) Maintainer: Lee S. McDaniel Author(s): Lee S. McDaniel, Jonathan S. Schildcrout License: GPL (>= 2) http://crantastic.org/packages/SOR Estimation for longitudinal data following outcome dependent sampling using the sequential offsetted regression technique. Includes support for binary, count, and continuous data. * spatialnbda (1.0) Maintainer: Glenna Nightingale Author(s): Glenna Nightingale License: GPL http://crantastic.org/packages/spatialnbda Network based diffusion analysis (NBDA) allows inference on the asocial and social transmission of information. This may involve the social transmission of a particular behaviour such as tool use, for example. For the NBDA, the key parameters estimated are the social effect and baseline rate parameters. The baseline rate parameter gives the rate at which the behaviour is first performed (or acquired) asocially amongst the individuals in a given population. The social effect parameter quantifies the effect of the social associations amongst the individuals on the rate at which each individual first performs or displays the behaviour. Spatial NBDA involves incorporating spatial information in the analysis. This is done by incorporating social networks derived from spatial point patterns (of the home bases of the individuals under study). In addition, a spatial covariate such as vegetation cover, or slope may be included in the modelling process. * UPMASK (1.0) Maintainer: Alberto Krone-Martins Author(s): Alberto Krone-Martins, Andre Moitinho License: GPL (>= 3) http://crantastic.org/packages/UPMASK An implementation of the UPMASK method for performing membership assignment in stellar clusters in R. It is prepared to use photometry and spatial positions, but it can take into account other types of data. The method is able to take into account arbitrary error models, and it is unsupervised, data-driven, physical-model-free and relies on as few assumptions as possible. The approach followed for membership assessment is based on an iterative process, principal component analysis, a clustering algorithm and a kernel density estimation. * uskewFactors (1.0) Maintainer: Paula M. Murray Author(s): Paula M. Murray, Ryan P. Browne, and Paul D. McNicholas License: GPL (>= 2) http://crantastic.org/packages/uskewFactors Implements mixtures of unrestricted skew-t factor analyzer models via the EM algorithm * vdmR (0.1.0) Maintainer: Tomokazu Fujino Author(s): Tomokazu Fujino License: GPL-2 http://crantastic.org/packages/vdmR This provides web based visual data mining tools by adding interactive functions to ggplot2 graphics. Brushing and linking between the multiple plots is one of the main feature of this package. Currently scatter plot, histogram, parallel coordinate plot and choropleth map are supported. Updated packages ---------------- allelematch (2.5), bbo (0.2), beanplot (1.2), betategarch (3.2), bReeze (0.4-0), coin (1.0-24), compute.es (0.2-4), corHMM (1.15), demography (1.18), DirichletReg (0.5-2), DirichletReg (0.5-1), Distance (0.9.2), dlm (1.1-4), dsm (2.2.5), fCopulae (3011.81), fmsb (0.5.1), fRegression (3011.81), gamlr (1.12), gamlss (4.3-1), gamlss.dist (4.3-1), gdsfmt (1.1.0.1), genlasso (1.3), geostatsp (1.0.0), geostatsp (1.0.1), gplots (2.14.2), GuardianR (0.5), intervals (0.15.0), investr (1.1.2), ivbma (1.05), LiblineaR (1.80-10), llama (0.7.2), LogicForest (2.1.0), mclust (4.4), mco (1.0.13), mitools (2.3), modTempEff (1.5.2), mrds (2.1.8), ncdf4 (1.13), nontarget (1.5), OrdLogReg (1.1), party (1.0-17), pcaPP (1.9-50), PerformanceAnalytics (1.4.3541), PivotalR (0.1.17.3), protViz (0.2.06), qat (0.73), qpcR (1.4-0), RadioSonde (1.4), RcppOctave (0.14.5), refGenome (1.3.0), repmis (0.3), rgdal (0.9-1), rms (4.2-1), rredis (1.6.9), RUnit (0.4.27), RVAideMemoire (0.9-39), shapes (1.1-10), SmoothHazard (1.2.0), SmoothHazard (1.2.3), spdep (0.5-77), spMC (0.3.4), SSDforR (1.4.7), Taxonstand (1.4), TreeSim (2.1) This email provided as a service for the R community by http://crantastic.org. 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