Sun, 09 Jun 2019

Package WgtEff updated to version 0.1.2 with previous version 0.1 dated 2019-05-30

Title: Functions for Weighting Effects
Description: Functions for determining the effect of data weights on the variance of survey data: users will load a data set which has a weights column, and the package will calculate the design effect (DEFF), weighting loss, root design effect (DEFT), effective sample size (ESS), and/or weighted margin of error.
Author: Joshua Miller [aut, cre]
Maintainer: Joshua Miller <joshlmiller@msn.com>

Diff between WgtEff versions 0.1 dated 2019-05-30 and 0.1.2 dated 2019-06-09

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More information about WgtEff at CRAN
Permanent link

Package sundialr updated to version 0.1.3 with previous version 0.1.2 dated 2019-01-12

Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computation.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE' and sensitivity calculator 'CVODES' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre], Scott D Cohen [ctb], Alan C Hindmarsh [ctb], Radu Serban [ctb], Dan Shumaker [ctb], Daniel R Reynolds [ctb], Aaron Collier [ctb], David Gardner [ctb], Carol Woodward [ctb], Slaven Peles [ctb], Peter Brown [ctb], Hilari C Tiedeman [ctb], Ting Yan [ctb], Lawrence Livermore National Security [cph], Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <sn248@cornell.edu>

Diff between sundialr versions 0.1.2 dated 2019-01-12 and 0.1.3 dated 2019-06-09

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Package installr updated to version 0.21.3 with previous version 0.21.0 dated 2018-10-06

Title: Using R to Install Stuff (Such As: R, 'Rtools', 'RStudio', 'Git', and More!)
Description: R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Barry Rowlingson [ctb], Boris Hejblum [ctb], Dason [ctb], Felix Schonbrodt [ctb], G. Grothendieck [ctb], GERGELY DAROCZI [ctb], Heuristic Andrew [ctb], James [ctb] (http://stackoverflow.com/users/269476/james), Thomas Leeper [ctb] (http://thomasleeper.com/), VitoshKa [ctb], Yihui Xie [ctb] (http://yihui.name), Michael Friendly [ctb] (http://datavis.ca/), Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/), Dieter Menne [ctb], Tyler Hunt [ctb] (https://github.com/JackStat), Takekatsu Hiramura [ctb] (https://github.com/hiratake55), Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool), Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey), Tom Allard [ctb], ChingChuan Chen [ctb], Jonathan Hill [ctb], Chan-Yub Park [ctb] (https://github.com/mrchypark), Gerhard Nachtmann [ctb]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package sim1000G updated to version 1.40 with previous version 1.39 dated 2018-03-10

Title: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Description: Generates realistic simulated genetic data in families or unrelated individuals.
Author: Apostolos Dimitromanolakis <apostolis@live.ca>, Jingxiong Xu <jingxiong.xu@mail.utoronto.ca>, Agnieszka Krol <krol@lunenfeld.ca>, Laurent Briollais <laurent@lunenfeld.ca>
Maintainer: Apostolos Dimitromanolakis <apostolis@live.ca>

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Package RSwissMaps updated to version 0.1.0.1 with previous version 0.1.0 dated 2017-10-02

Title: Plot and Save Customised Swiss Maps
Description: Allows to link data to Swiss administrative divisions (municipalities, districts, cantons) and to plot and save customised maps thereof. Furthermore, the package allows to generate tailored templates for data collection. The used geodata is publicly available on the Swiss Federal Statistical Office website <https://www.bfs.admin.ch/bfs/de/home/dienstleistungen/geostat/geodaten-bundesstatistik.html>.
Author: David Zumbach [aut, cre]
Maintainer: David Zumbach <david.zumbach@gfzb.ch>

Diff between RSwissMaps versions 0.1.0 dated 2017-10-02 and 0.1.0.1 dated 2019-06-09

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Package rrecsys updated to version 0.9.7.3.1 with previous version 0.9.7.3 dated 2018-02-10

Title: Environment for Evaluating Recommender Systems
Description: Processes standard recommendation datasets (e.g., a user-item rating matrix) as input and generates rating predictions and lists of recommended items. Standard algorithm implementations which are included in this package are the following: Global/Item/User-Average baselines, Weighted Slope One, Item-Based KNN, User-Based KNN, FunkSVD, BPR and weighted ALS. They can be assessed according to the standard offline evaluation methodology (Shani, et al. (2011) <doi:10.1007/978-0-387-85820-3_8>) for recommender systems using measures such as MAE, RMSE, Precision, Recall, F1, AUC, NDCG, RankScore and coverage measures. The package (Coba, et al.(2017) <doi: 10.1007/978-3-319-60042-0_36>) is intended for rapid prototyping of recommendation algorithms and education purposes.
Author: Ludovik Çoba [aut, cre, cph], Markus Zanker [ctb], Panagiotis Symeonidis [ctb]
Maintainer: Ludovik Çoba <Ludovik.Coba@inf.unibz.it>

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Package rLakeAnalyzer updated to version 1.11.4.1 with previous version 1.11.4 dated 2018-03-14

Title: Lake Physics Tools
Description: Standardized methods for calculating common important derived physical features of lakes including water density based based on temperature, thermal layers, thermocline depth, lake number, Wedderburn number, Schmidt stability and others.
Author: Luke Winslow, Jordan Read, Richard Woolway, Jennifer Brentrup, Taylor Leach, Jake Zwart, Sam Albers, Doug Collinge
Maintainer: Luke Winslow <lawinslow@gmail.com>

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Package Ricetl updated to version 0.2.5.1 with previous version 0.2.5 dated 2018-03-21

Title: Data Extraction for People's Republic of China Resident Identity Card
Description: People's Republic of China resident identity card contains a lot of personal information. It can extract the location of the household's residence in the identity card, the date of birth, the sex, the location of the registered police station, and can identify the authenticity of the ID card through the check code. 'Ricetl' provides graphical user interface to process the function of extracting the above effective private information in the ID card number, and provides a public data set related to the ID number.
Author: Xu Jing [aut, cre]
Maintainer: Xu Jing <274762204@qq.com>

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Package mwshiny updated to version 1.0.0 with previous version 0.1.0 dated 2019-03-06

Title: 'Shiny' for Multiple Windows
Description: A simple function, mwsApp(), that runs a 'shiny' app spanning multiple, connected windows. This uses all standard 'shiny' conventions, and depends only on the 'shiny' package.
Author: Hannah De los Santos [aut, cre], John Erickson [aut], Nicholas Thomson [ctb], Kristin Bennett [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>

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Package econullnetr updated to version 0.1.0.1 with previous version 0.1.0 dated 2017-09-25

Title: Null Model Analysis for Ecological Networks
Description: Tools for using null models to analyse ecological networks (e.g. food webs, flower-visitation networks, seed-dispersal networks) and detect resource preferences or non-random interactions among network nodes. Tools are provided to run null models, test for and plot preferences, plot and analyse bipartite networks, and export null model results in a form compatible with other network analysis packages. The underlying null model was developed by Agusti et al. (2003) <doi:10.1046/j.1365-294X.2003.02014.x> and the full application to ecological networks by Vaughan et al. (2017) econullnetr: an R package using null models to analyse the structure of ecological networks and identify resource selection. Methods in Ecology & Evolution, in press.
Author: Ian Vaughan
Maintainer: Ian Vaughan <vaughanip@cardiff.ac.uk>

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Package datasus updated to version 0.4.1.1 with previous version 0.4.1 dated 2018-05-16

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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Package ChemoSpec updated to version 5.1.9 with previous version 5.0.229 dated 2019-03-01

Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of 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 for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

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Package bioacoustics updated to version 0.2.0.1 with previous version 0.2.0 dated 2019-02-08

Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), David Riggs [ctb, cph] (Read GUANO metadata, original R code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, inc. [ctb, cph] (Read WAC files, original C code), WavX, inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>

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Package hablar updated to version 0.2.0 with previous version 0.1.0 dated 2018-10-26

Title: Non-Astonishing Results in R
Description: Simple tools for converting columns to new data types. Intuitive functions for columns with missing values.
Author: David Sjoberg
Maintainer: David Sjoberg <dav.sjob@gmail.com>

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Package ChemoSpec2D updated to version 0.3.166 with previous version 0.2.19 dated 2019-03-01

Title: Exploratory Chemometrics for 2D Spectroscopy
Description: A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

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Package penaltyLearning updated to version 2019.5.29 with previous version 2018.09.04 dated 2018-09-10

Title: Penalty Learning
Description: Implementations of algorithms from Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression, by Hocking, Rigaill, Vert, Bach <http://proceedings.mlr.press/v28/hocking13.html> published in proceedings of ICML2013.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>

Diff between penaltyLearning versions 2018.09.04 dated 2018-09-10 and 2019.5.29 dated 2019-06-09

 DESCRIPTION                                    |   12 
 MD5                                            |   61 
 NAMESPACE                                      |   27 
 NEWS                                           |  290 ++--
 R/IntervalRegression.R                         | 1756 ++++++++++++-------------
 R/ROChange.R                                   |  373 +++--
 R/featureVector.R                              |  214 +--
 R/geoms.R                                      |  142 +-
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 R/modelSelection.R                             |  524 ++++---
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Package littler updated to version 0.3.8 with previous version 0.3.7 dated 2019-03-15

Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between littler versions 0.3.7 dated 2019-03-15 and 0.3.8 dated 2019-06-09

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Package gss updated to version 2.1-10 with previous version 2.1-9 dated 2018-05-06

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

Diff between gss versions 2.1-9 dated 2018-05-06 and 2.1-10 dated 2019-06-09

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New package motmot with initial version 2.1.2
Package: motmot
Type: Package
Title: Models of Trait Macroevolution on Trees
Version: 2.1.2
Depends: R (>= 2.10.0), ape (>= 3.0-7)
Date: 2019-06-02
Author: Mark Puttick [aut, cre, cph], Gavin Thomas [aut, cph], Rob Freckleton [aut, cph], Magnus Clarke [ctb], Travis Ingram [ctb], David Orme [ctb], Emmanuel Paradis [ctb]
Maintainer: Mark Puttick <marknputtick@gmail.com>
Description: Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2011) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.
License: GPL (>= 2)
Repository: CRAN
URL: https://puttickbiology.wordpress.com/motmot/
RoxygenNote: 6.1.1
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LinkingTo: Rcpp
Imports: Rcpp, coda, ks, mvtnorm, caper, methods
Encoding: UTF-8
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2019-06-09 08:01:44 UTC; markputtick
Date/Publication: 2019-06-09 16:00:02 UTC

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Package lcopula updated to version 1.0.3 with previous version 1.0 dated 2017-02-01

Title: Liouville Copulas
Description: Collections of functions allowing random number generations and estimation of 'Liouville' copulas.
Author: Leo Belzile [aut, cre], Christian Genest [aut, ctb], Alexander J. McNeil [ctb], Johanna G. Neslehova [ctb]
Maintainer: Leo Belzile <belzilel@gmail.com>

Diff between lcopula versions 1.0 dated 2017-02-01 and 1.0.3 dated 2019-06-09

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Package clusterSEs updated to version 2.6.1 with previous version 2.6 dated 2019-06-09

Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller (2010) <DOI:10.1198/jbes.2009.08046>, pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller (2008) <DOI:10.1162/rest.90.3.414>. Procedures are included for use with GLM, ivreg, plm (pooling or fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>

Diff between clusterSEs versions 2.6 dated 2019-06-09 and 2.6.1 dated 2019-06-09

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More information about clusterSEs at CRAN
Permanent link

Package ChemoSpecUtils updated to version 0.3.20 with previous version 0.2.211 dated 2019-03-01

Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

Diff between ChemoSpecUtils versions 0.2.211 dated 2019-03-01 and 0.3.20 dated 2019-06-09

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Permanent link

Package BMAmevt updated to version 1.0.3 with previous version 1.0.1 dated 2017-03-06

Title: Multivariate Extremes: Bayesian Estimation of the Spectral Measure
Description: Toolkit for Bayesian estimation of the dependence structure in multivariate extreme value parametric models.
Author: Anne Sabourin
Maintainer: Leo Belzile <belzilel@gmail.com>

Diff between BMAmevt versions 1.0.1 dated 2017-03-06 and 1.0.3 dated 2019-06-09

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Package kstMatrix updated to version 0.1-2 with previous version 0.1-1 dated 2019-03-27

Title: Basic Functions in Knowledge Space Theory Using Matrix Representation
Description: Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical framework, which proposes mathematical formalisms to operationalize knowledge structures in a particular domain. The 'kstMatrix' package provides basic functionalities to generate, handle, and manipulate knowledge structures and knowledge spaces. Opposed to the 'kst' package, 'kstMatrix' uses matrix representations for knowledge structures. Furthermore, 'kstMatrix' contains several knowledge spaces developed by the research group around Cornelia Dowling through querying experts.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>

Diff between kstMatrix versions 0.1-1 dated 2019-03-27 and 0.1-2 dated 2019-06-09

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Package maditr updated to version 0.6.2 with previous version 0.6.1 dated 2019-01-03

Title: Fast Data Aggregation, Modification, and Filtering with Pipes and 'data.table'
Description: Package provides pipe-style interface for 'data.table'. It preserves all 'data.table' features without significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data manipulation tasks. For example, you can write 'mtcars %>% take(mean(mpg), by = am)' for aggregation or 'mtcars %>% let(hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional aggregation/modification. 'query_if' function translates its arguments one-to-one to '[.data.table' method. Additionally there are some conveniences such as automatic 'data.frame' conversion to 'data.table'.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>

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Package plothelper updated to version 0.1.2 with previous version 0.1.1 dated 2019-04-22

Title: New Plots Based on 'ggplot2' and Functions to Create Regular Shapes
Description: An extension to 'ggplot2' with miscellaneous functions. It contains two groups of functions: Functions in the first group draw 'ggplot2' - based plots: gg_shading_bar() draws barplot with shading colors in each bar. geom_rect_cm(), geom_circle_cm() and geom_ellipse_cm() draw rectangles, circles and ellipses with centimeter as their unit. Thus their sizes do not change when the coordinate system or the aspect ratio changes. Functions in the second group generate coordinates for regular shapes and make linear transformations.
Author: Jiang Wu [aut, cre] (from Capital Normal University)
Maintainer: Jiang Wu <textidea@sina.com>

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Package missRanger updated to version 1.0.5 with previous version 1.0.4 dated 2019-01-07

Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest' algorithm used to impute mixed-type data sets by chaining random forests, introduced by Stekhoven, D.J. and Buehlmann, P. (2012) <doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the lightning fast random jungle package 'ranger'. Between the iterative model fitting, we offer the option of using predictive mean matching. This firstly avoids imputation with values not already present in the original data (like a value 0.3334 in 0-1 coded variable). Secondly, predictive mean matching tries to raise the variance in the resulting conditional distributions to a realistic level. This would allow e.g. to do multiple imputation when repeating the call to missRanger().
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

Diff between missRanger versions 1.0.4 dated 2019-01-07 and 1.0.5 dated 2019-06-09

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Package clusterSEs updated to version 2.6 with previous version 2.5.1 dated 2018-10-29

Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller (2010) <DOI:10.1198/jbes.2009.08046>, pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller (2008) <DOI:10.1162/rest.90.3.414>. Procedures are included for use with GLM, ivreg, plm (pooling or fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>

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Package assignPOP updated to version 1.1.6 with previous version 1.1.4 dated 2018-03-13

Title: Population Assignment using Genetic, Non-Genetic or Integrated Data in a Machine Learning Framework
Description: Use Monte-Carlo and K-fold cross-validation coupled with machine- learning classification algorithms to perform population assignment, with functionalities of evaluating discriminatory power of independent training samples, identifying informative loci, reducing data dimensionality for genomic data, integrating genetic and non-genetic data, and visualizing results.
Author: Kuan-Yu (Alex) Chen [aut, cre], Elizabeth A. Marschall [aut], Michael G. Sovic [aut], Anthony C. Fries [aut], H. Lisle Gibbs [aut], Stuart A. Ludsin [aut]
Maintainer: Kuan-Yu (Alex) Chen <alexkychen@gmail.com>

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