Wed, 25 Apr 2018

Package survivALL updated to version 0.9.3 with previous version 0.9.2 dated 2018-03-01

Title: Continuous Biomarker Assessment by Exhaustive Survival Analysis
Description: In routine practice, biomarker performance is calculated by splitting a patient cohort at some arbitrary level, often by median gene expression. The logic behind this is to divide patients into “high” or “low” expression groups that in turn correlate with either good or poor prognosis. However, this median-split approach assumes that the data set composition adheres to a strict 1:1 proportion of high vs. low expression, that for every one “low” there is an equivalent “high”. In reality, data sets are often heterogeneous in their composition (Perou, CM et al., 2000 <doi:10.1038/35021093>)- i.e. this 1:1 relationship is unlikely to exist and the true relationship unknown. Given this limitation, it remains difficult to determine where the most significant separation should be made. For example, estrogen receptor (ER) status determined by immunohistochemistry is standard practice in predicting hormone therapy response, where ER is found in an ~1:3 ratio (-:+) in the population (Selli, C et al., 2016 <doi:10.1186/s13058-016-0779-0>). We would expect therefore, upon dividing patients by ER expression, 25% to be classified “low” and 75% “high”, and an otherwise 50-50 split to incorrectly classify 25% of our patient cohort, rendering our survival estimate under powered. 'survivALL' is a data-driven approach to calculate the relative survival estimates for all possible points of separation - i.e. at all possible ratios of “high” vs. “low” - allowing a measure’s relationship with survival to be more reliably determined and quantified. We see this as a solution to a flaw in common research practice, namely the failure of a true biomarker as part of a meta-analysis.
Author: Dominic Pearce [aut, cre]
Maintainer: Dominic Pearce <dominic.pearce@ed.ac.uk>

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Package lvnet updated to version 0.3.3 with previous version 0.3.2 dated 2017-09-02

Title: Latent Variable Network Modeling
Description: Estimate, fit and compare Structural Equation Models (SEM) and network models (Gaussian Graphical Models; GGM) using OpenMx. Allows for two possible generalizations to include GGMs in SEM: GGMs can be used between latent variables (latent network modeling; LNM) or between residuals (residual network modeling; RNM). For details, see Epskamp, Rhemtulla and Borsboom (2017) <doi:10.1007/s11336-017-9557-x>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package sjlabelled updated to version 1.0.10 with previous version 1.0.9 dated 2018-04-24

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package PAFit updated to version 1.0.0.4 with previous version 1.0.0.3 dated 2018-02-05

Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <10.1371/journal.pone.0137796>. Thong Pham et al.(2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>

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Package lavaanPlot updated to version 0.5.1 with previous version 0.3.0 dated 2018-01-26

Title: Path Diagrams for Lavaan Models via DiagrammeR
Description: Plots path diagrams from models in lavaan using the plotting functionality from the DiagrammeR package. DiagrammeR provides nice path diagrams via Graphviz, and these functions make it easy to generate these diagrams from a lavaan path model without having to write the DOT language graph specification.
Author: Alex Lishinski
Maintainer: Alex Lishinski <alexlishinski@gmail.com>

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Package forestmodel updated to version 0.5.0 with previous version 0.4.3 dated 2017-04-16

Title: Forest Plots from Regression Models
Description: Produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>

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Package base2grob updated to version 0.0.3 with previous version 0.0.2 dated 2018-03-15

Title: Convert Base Plot to 'grob' Object
Description: Convert base plot function call (using expression or formula) to 'grob' object that compatible to the 'grid' ecosystem. With this package, we are able to e.g. using 'cowplot' to align base plots with 'ggplot' objects and using 'ggsave' to export base plot to file.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package ztable updated to version 0.1.8 with previous version 0.1.5 dated 2015-02-15

Title: Zebra-Striped Tables in LaTeX and HTML Formats
Description: Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>

Diff between ztable versions 0.1.5 dated 2015-02-15 and 0.1.8 dated 2018-04-25

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Tue, 24 Apr 2018

Package sourcetools updated to version 0.1.7 with previous version 0.1.6 dated 2017-04-05

Title: Tools for Reading, Tokenizing and Parsing R Code
Description: Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.
Author: Kevin Ushey
Maintainer: Kevin Ushey <kevinushey@gmail.com>

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Package edpclient updated to version 0.5.1 with previous version 0.3.1 dated 2018-03-05

Title: Empirical Data Platform Client
Description: R client for Empirical Data Platform. More information is at <https://empirical.com>. For support, contact support@empirical.com.
Author: Empirical Engineering
Maintainer: Madeleine Thompson <madeleine@empirical.com>

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Package sjlabelled updated to version 1.0.9 with previous version 1.0.8 dated 2018-02-26

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package robustbase updated to version 0.93-0 with previous version 0.92-8 dated 2017-11-01

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre], Peter Rousseeuw [ctb] (Qn and Sn), Christophe Croux [ctb] (Qn and Sn), Valentin Todorov [aut] (most robust Cov), Andreas Ruckstuhl [aut] (nlrob, anova, glmrob), Matias Salibian-Barrera [aut] (lmrob orig.), Tobias Verbeke [ctb, fnd] (mc, adjbox), Manuel Koller [aut] (lmrob, psi-func.), Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob), Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package rly updated to version 1.6.1 with previous version 1.5 dated 2018-03-26

Title: 'Lex' and 'Yacc'
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph], Yasutaka Tanaka [ctb], Henrico Witvliet [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>

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Package sigr updated to version 0.2.5 with previous version 0.2.4 dated 2018-03-13

Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting and planning of experimental results, working around issue such as the difficulty of extracting model summary facts (such as with 'lm'/'glm'). This package also includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package languageserver updated to version 0.2.1 with previous version 0.2.0 dated 2018-04-24

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package water updated to version 0.8 with previous version 0.7 dated 2017-10-15

Title: Actual Evapotranspiration with Energy Balance Models
Description: Tools and functions to calculate actual Evapotranspiration using surface energy balance models.
Author: Guillermo Federico Olmedo [aut, cre], Samuel Ortega-Farías [aut], David Fonseca-Luengo [aut], Daniel de la Fuente-Sáiz [aut], Fernando Fuentes Peñailillo [aut], María Victoria Munafó [ctb]
Maintainer: Guillermo Federico Olmedo <guillermo.olmedo@gmail.com>

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Package sn updated to version 1.5-2 with previous version 1.5-1 dated 2017-11-22

Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and model diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package PieceExpIntensity updated to version 1.0.4 with previous version 1.0.2 dated 2018-03-28

Title: Bayesian Model to Find Changepoints Based on Rates and Count Data
Description: This function fits a reversible jump Bayesian piecewise exponential model that also includes the intensity of each event considered along with the rate of events.
Author: Andrew G. Chapple
Maintainer: Andrew G. Chapple <agc6@rice.edu>

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Package MARX updated to version 0.2 with previous version 0.1 dated 2017-06-16

Title: Simulation, Estimation, Model Selection and Forecasting for MARX Models
Description: Simulate, estimate (by t-MLE), select and forecast mixed causal-noncausal autoregressive models with possibly exogenous regressors, using methods proposed in Lanne and Saikkonen (2011) <doi:10.2202/1941-1928.1080> and Hecq et al. (2016) <doi:10.15609/annaeconstat2009.123-124.0307>.
Author: Sean Telg [aut, cre, cph], Alain Hecq [ctb], Lenard Lieb [ctb]
Maintainer: Sean Telg <j.telg@maastrichtuniversity.nl>

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Package mdmb updated to version 0.7-19 with previous version 0.6-17 dated 2018-02-16

Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005; <doi:10.1198/016214504000001844>). The regression model can be nonlinear (e.g., including interaction or quadratic effects). Multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package hrbrthemes updated to version 0.5.0 with previous version 0.1.0 dated 2017-02-26

Title: Additional Themes, Theme Components and Utilities for 'ggplot2'
Description: A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' <https://github.com/google/roboto/> is also included along with a copy of the 'IBM' 'Plex Sans' <https://github.com/IBM/type> and 'Titillium Web' <https://fonts.google.com/specimen/Titillium+Web> fonts are also included to support their respective typography-oriented themes.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Patrick Kennedy [ctb], Philipp Reiner [ctb], Dan Wilson [ctb] (Secondary axis support), Xavier Adam [ctb], Google [cph] (Roboto Condensed & Titillium Web Fonts), IBM [cph] (Plex Sans Font), Jacob Barnett [ctb], Thomas J. Leeper [ctb] (<https://orcid.org/0000-0003-4097-6326>)
Maintainer: Bob Rudis <bob@rud.is>

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Package bigrquery updated to version 1.0.0 with previous version 0.4.1 dated 2017-06-26

Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre], Kungliga Tekniska Högskolan [ctb] (strptime implementation), The NetBSD Foundation, Inc. [ctb] (gmtime implementation), RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package textclean updated to version 0.7.3 with previous version 0.7.2 dated 2018-04-19

Title: Text Cleaning Tools
Description: Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) <doi:10.1006/csla.2001.0169>) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The 'replace_emoticon()' function replaces emoticons with word equivalents.
Author: Tyler Rinker [aut, cre], ctwheels StackOverflow [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between textclean versions 0.7.2 dated 2018-04-19 and 0.7.3 dated 2018-04-24

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Package SNFtool updated to version 2.3.0 with previous version 2.2.1 dated 2017-11-24

Title: Similarity Network Fusion
Description: Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.
Author: Bo Wang, Aziz Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg
Maintainer: Daniel Cole <goldenberglab@gmail.com>

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Package sentimentr updated to version 2.3.2 with previous version 2.2.3 dated 2018-01-16

Title: Calculate Text Polarity Sentiment
Description: Calculate text polarity sentiment at the sentence level and optionally aggregate by rows or grouping variable(s).
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

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Package epitrix updated to version 0.2.0 with previous version 0.1.2 dated 2018-03-01

Title: Small Helpers and Tricks for Epidemics Analysis
Description: A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymise data, and fitting discretised Gamma distributions.
Author: Thibaut Jombart [aut, cre], Anne Cori [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

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Package detrendr updated to version 0.5.1 with previous version 0.5.0 dated 2018-04-19

Title: Detrend Images
Description: Image series affected by bleaching must be corrected by 'detrending' prior to the performance of quantitative analysis. 'detrendr' is for correctly detrending images. It uses Nolan's algorithm (Nolan et al., 2017 <doi:10.1093/bioinformatics/btx434>).
Author: Rory Nolan [aut, cre, cph], Sergi Padilla-Parra [ths, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package nmfem updated to version 1.0.3 with previous version 1.0.2 dated 2018-04-23

Title: NMF-EM Algorithm
Description: Provides a version of the Expectation-Maximization algorithm for mix-models, reducing the numbers of parameters to estimate using Non-negative Matrix Factorization methods. For more explanations, see pre-print of Carel and Alquier (2017) <arXiv:1709.03346>.
Author: Lena Carel [aut, cre]
Maintainer: Lena Carel <lena.carel@gmail.com>

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Package VarReg updated to version 1.0.2 with previous version 1.0.1 dated 2017-05-30

Title: Semi-Parametric Variance Regression
Description: Methods for fitting semi-parametric mean and variance models, with normal or censored data. Also extended to allow a regression in the location, scale and shape parameters.
Author: Kristy Robledo [aut, cre], Ian Marschner [ths]
Maintainer: Kristy Robledo <robledo.kristy@gmail.com>

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Package tstools updated to version 0.3.6.1 with previous version 0.3.6 dated 2018-03-13

Title: A Time Series Toolbox for Official Statistics
Description: Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.
Author: Matthias Bannert [aut, cre], Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>

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Package provenance updated to version 2.0 with previous version 1.9 dated 2018-01-02

Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances, and point-counting data with the chi-square distance. Also included are tools to plot compositional and point-counting data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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Package survival updated to version 2.42-3.1 with previous version 2.42-3 dated 2018-04-16

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

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Package upwaver updated to version 1.1.0 with previous version 1.0.1 dated 2018-01-22

Title: Access 'Upwave' API
Description: 'Upwave' <https://www.upwave.io/> is a task management app organising tasks on boards and cards. 'upwaver' is a wrapper around the 'Upwave' API <https://upwavehq.github.io/api/> that allows listing and updating those boards and cards.
Author: Adrian Staempfli, Christoph Strauss, Fabian Leuthold, Michael Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>

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Package RSMET updated to version 1.3.8 with previous version 1.2.9 dated 2016-03-17

Title: Get Real-Time Meteorological Data in SMET Format
Description: It manages snow and weather local time series as provided by MeteoIO (<http://models.slf.ch/docserver/meteoio/html/index.html>, <http:// www.slf.ch/ueber/organisation/schnee_permafrost/projekte/MeteoIO/index_EN>, <https://www.openhub.net/p/MeteoIO>). MeteoIO is a C/C++ Open Source library which has been designed to settle both the needs of carefully crafted simulations for a specific purpose/study and for the needs of operational simulations that run automatically and unattended". It is integrated in physical spatially-distributed models and tackles several issues with weather input/ output data. Here a SMET S4 class object is defined and can be imported from/ exported to a SMET ini files of MeteoIO , allowing interoperability from R to MeteoIO and other SMET-compliant software.
Author: Emanuele Cordano
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>

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Package margins updated to version 0.3.20 with previous version 0.3.0 dated 2017-03-22

Title: Marginal Effects for Model Objects
Description: An R port of Stata's 'margins' command, which can be used to calculate marginal (or partial) effects from model objects.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>), Jeffrey Arnold [ctb], Vincent Arel-Bundock [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package immer updated to version 1.0-138 with previous version 0.8-5 dated 2017-04-27

Title: Item Response Models for Multiple Ratings
Description: Implements some item response models for multiple ratings, including the hierarchical rater model, conditional maximum likelihood estimation of linear logistic partial credit model and a wrapper function to the commercial FACETS program. See Robitzsch and Steinfeld (2018) for a description of the functionality of the package.
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package EpiCurve updated to version 2.1-1 with previous version 2.0-1 dated 2017-08-24

Title: Plot an Epidemic Curve
Description: Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
Author: Jean Pierre Decorps [aut, cre], Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>

Diff between EpiCurve versions 2.0-1 dated 2017-08-24 and 2.1-1 dated 2018-04-24

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Package BayesXsrc updated to version 3.0-1 with previous version 3.0-0 dated 2018-02-22

Title: R Package Distribution of the BayesX C++ Sources
Description: BayesX performs Bayesian inference in structured additive regression (STAR) models. The R package BayesXsrc provides the BayesX command line tool for easy installation. A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre], Daniel Adler [aut], Thomas Kneib [aut], Stefan Lang [aut], Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

Diff between BayesXsrc versions 3.0-0 dated 2018-02-22 and 3.0-1 dated 2018-04-24

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Package archivist updated to version 2.3.1 with previous version 2.3 dated 2018-02-19

Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut], Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between archivist versions 2.3 dated 2018-02-19 and 2.3.1 dated 2018-04-24

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Package SourceSet updated to version 0.1.1 with previous version 0.1.0 dated 2018-02-28

Title: A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways
Description: The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')').
Author: Elisa Salviato [aut, cre], Vera Djordjilovic [aut], Chiara Romualdi [aut], Monica Chiogna [aut]
Maintainer: Elisa Salviato <elisa.salviato.88@gmail.com>

Diff between SourceSet versions 0.1.0 dated 2018-02-28 and 0.1.1 dated 2018-04-24

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Package DDD updated to version 3.7 with previous version 3.6 dated 2018-02-07

Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>. Also contains functions to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

Diff between DDD versions 3.6 dated 2018-02-07 and 3.7 dated 2018-04-24

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Package aroma.core updated to version 3.1.2 with previous version 3.1.1 dated 2017-09-13

Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between aroma.core versions 3.1.1 dated 2017-09-13 and 3.1.2 dated 2018-04-24

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 R/CbsModel.R                                                |   36 
 R/CbsSegmentationDataFile.R                                 |   16 
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 R/RawGenomicSignals.OPS.R                                   |   91 
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 R/RawGenomicSignals.R                                       | 2496 ++--
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 R/fitSplineBlockPolish.matrix.R                             |   23 
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 R/normalizeGenotypeCone.R                                   |   16 
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 R/remap.R                                                   |   77 
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 R/smoothWSA.matrix.R                                        |  260 
 R/stextChipType.R                                           |    9 
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 R/transforms.R                                              |   75 
 R/utils.R                                                   |only
 R/yellow.colors.R                                           |   11 
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 tests/RawCopyNumbers,states.R                               |  130 
 tests/RawCopyNumbers.R                                      |  256 
 tests/RawGenomicSignals.SEG.R                               |    9 
 tests/RichDataFrame.R                                       |  122 
 tests/SegmentedCopyNumbers.R                                |  196 
 196 files changed, 30052 insertions(+), 34623 deletions(-)

More information about aroma.core at CRAN
Permanent link

Package FRegSigCom updated to version 0.2.1 with previous version 0.1.0 dated 2017-09-06

Title: Functional Regression using Signal Compression Approach
Description: Signal compression methods for function-on-function (FOF) regression with functional response and functional predictors, including linear models with both scalar and functional predictors for a small number of functional predictors, linear models with functional predictors for a large number of functional predictors, stepwise selection for FOF models with two-way interactions, and nonlinear models. References are linked to via the URL below.
Author: Ruiyan Luo, Xin Qi
Maintainer: Ruiyan Luo <rluo@gsu.edu>

Diff between FRegSigCom versions 0.1.0 dated 2017-09-06 and 0.2.1 dated 2018-04-24

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More information about FRegSigCom at CRAN
Permanent link

Package dglars updated to version 2.0.1 with previous version 2.0.0 dated 2017-02-28

Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

Diff between dglars versions 2.0.0 dated 2017-02-28 and 2.0.1 dated 2018-04-24

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More information about dglars at CRAN
Permanent link

Package lexicon updated to version 1.0.0 with previous version 0.7.4 dated 2018-01-13

Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and word lists.
Author: Tyler Rinker [aut, cre, cph], University of Notre Dame [dtc, cph], Department of Knowledge Technologies [dtc, cph], Unicode, Inc. [dtc, cph], John Higgins [dtc, cph], Grady Ward [dtc], Heiko Possel [dtc], Michal Boleslav Mechura [dtc, cph], Bing Liu [dtc], Minqing Hu [dtc], Saif M. Mohammad [dtc], Peter Turney [dtc], Erik Cambria [dtc], Soujanya Poria [dtc], Rajiv Bajpai [dtc], Bjoern Schuller [dtc], SentiWordNet [dtc, cph], Liang Wu [dtc, cph], Fred Morstatter [dtc, cph], Huan Liu [dtc, cph], Grammar Revolution [dtc, cph], Vidar Holen [dtc, cph], Alejandro U. Alvarez [dtc, cph], Stackoverflow User user2592414 [dtc, cph], BannedWordList.com [dtc, cph], Apache Software Foundation [dtc, cph], Andrew Kachites McCallum [dtc, cph], Alireza Savand [dtc, cph]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

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More information about lexicon at CRAN
Permanent link

Package languageserver updated to version 0.2.0 with previous version 0.1.0 dated 2018-03-01

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between languageserver versions 0.1.0 dated 2018-03-01 and 0.2.0 dated 2018-04-24

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More information about languageserver at CRAN
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Package iterpc updated to version 0.4.0 with previous version 0.3.4 dated 2017-12-06

Title: Efficient Iterator for Permutations and Combinations
Description: Iterator for generating permutations and combinations. They can be either drawn with or without replacement, or with distinct/ non-distinct items (multiset). The generated sequences are in lexicographical order (dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer being maintained. Users are recommended to switch to 'arrangements'.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between iterpc versions 0.3.4 dated 2017-12-06 and 0.4.0 dated 2018-04-24

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More information about iterpc at CRAN
Permanent link

Package arulesViz updated to version 1.3-1 with previous version 1.3-0 dated 2017-09-09

Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler [aut, cre, cph], Giallanza Tyler [ctb], Sudheer Chelluboina [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between arulesViz versions 1.3-0 dated 2017-09-09 and 1.3-1 dated 2018-04-24

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More information about arulesViz at CRAN
Permanent link

Mon, 23 Apr 2018

Package JuniperKernel updated to version 1.4.0.0 with previous version 1.2.3.0 dated 2018-02-05

Title: Kernel for 'Jupyter'
Description: Provides a full implementation of the 'Jupyter' <http://jupyter.org/> messaging protocol in C++ by leveraging 'Rcpp' and 'Xeus' <https://github.com/QuantStack/xeus>. 'Jupyter' supplies an interactive computing environment and a messaging protocol defined over 'ZeroMQ' for multiple programming languages. This package implements the 'Jupyter' kernel interface so that 'R' is exposed to this interactive computing environment. 'ZeroMQ' functionality is provided by the 'pbdZMQ' package. 'Xeus' is a C++ library that facilitates the implementation of kernels for 'Jupyter'. Additionally, 'Xeus' provides an interface to libraries that exist in the 'Jupyter' ecosystem for building widgets, plotting, and more <https://blog.jupyter.org/interactive-workflows-for-c-with-jupyter-fe9b54227d92>. 'JuniperKernel' uses 'Xeus' as a library for the 'Jupyter' messaging protocol.
Author: Spencer Aiello [aut, cre, cph], Wei-Chen Chen [ctb], Stephan Brumme [cph], Jake Luciani [cph], Tony Plate [cph], Matthieu Decorde [cph], RStudio (Hadley Wickham) [cph], Sylvain Corlay [cph], Johan Mabille [cph], Niels Lohmann [cph]
Maintainer: Spencer Aiello <spnrpa@gmail.com>

Diff between JuniperKernel versions 1.2.3.0 dated 2018-02-05 and 1.4.0.0 dated 2018-04-23

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More information about JuniperKernel at CRAN
Permanent link

Package d3r updated to version 0.8.1 with previous version 0.8.0 dated 2018-03-17

Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kent Russell [aut, cre] (R interface), Gregor Aisch [aut, cph] (d3-jetpack creator, https://github.com/gka/d3-jetpack), Adam Pearce [aut] (core contributor to d3-jetpack), Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between d3r versions 0.8.0 dated 2018-03-17 and 0.8.1 dated 2018-04-23

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More information about d3r at CRAN
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Package lmerTest updated to version 3.0-1 with previous version 3.0-0 dated 2018-04-16

Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.
Author: Alexandra Kuznetsova [aut], Per Bruun Brockhoff [aut, ths, cre], Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>

Diff between lmerTest versions 3.0-0 dated 2018-04-16 and 3.0-1 dated 2018-04-23

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More information about lmerTest at CRAN
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Package leaflet.esri updated to version 1.0.0 with previous version 0.2 dated 2017-06-25

Title: 'ESRI' Bindings for the 'leaflet' Package
Description: An add-on package to the 'leaflet' package, which provides bindings for 'ESRI' services. This package allows a user to add 'ESRI' provided services such as 'MapService', 'ImageMapService', 'TiledMapService' etc. to a 'leaflet' map.
Author: Bhaskar Karambelkar [aut, cre], Barret Schloerke [aut], Patrick Arlt [ctb, cph] (esri-leaflet, esri-leaflet-cluster, esri-leaflet-geocoder, and esri-leaflet-heatmap libraries), Rachel Nehmer [ctb, cph] (esri-leaflet-renderers library), Vladimir Agafonkin [ctb, cph] (leaflet.heat and simpleheat libraries), Leaflet [ctb, cph] (leaflet.markercluster library)
Maintainer: Bhaskar Karambelkar <bhaskarvk@gmail.com>

Diff between leaflet.esri versions 0.2 dated 2017-06-25 and 1.0.0 dated 2018-04-23

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More information about leaflet.esri at CRAN
Permanent link

Package arulesCBA updated to version 1.1.3-1 with previous version 1.1.3 dated 2018-03-07

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 [aut, cph]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>

Diff between arulesCBA versions 1.1.3 dated 2018-03-07 and 1.1.3-1 dated 2018-04-23

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Permanent link

Package HRM updated to version 0.9.1 with previous version 0.8.0 dated 2018-02-14

Title: High-Dimensional Repeated Measures
Description: Methods for testing main and interaction effects in possibly high-dimensional parametric or nonparametric repeated measures in factorial designs. The observations of the subjects are assumed to be multivariate normal if using the parametric test. The nonparametric version tests with regard to nonparametric relative effects (based on pseudo-ranks). It is possible to use up to 2 whole- and 3 subplot factors.
Author: Martin Happ [aut, cre], Harrar W. Solomon [aut], Arne C. Bathke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>

Diff between HRM versions 0.8.0 dated 2018-02-14 and 0.9.1 dated 2018-04-23

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Package komadown updated to version 0.2.0 with previous version 0.1.0 dated 2017-08-20

Title: R Markdown Templates for the 'KOMA-Script' Classes
Description: R Markdown templates based on the 'KOMA-Script' classes for LaTeX, additionally offering cross-referencing via the 'bookdown' package.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>)
Maintainer: Johan Larsson <johanlarsson@outlook.com>

Diff between komadown versions 0.1.0 dated 2017-08-20 and 0.2.0 dated 2018-04-23

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Package sigmaNet updated to version 1.1.0 with previous version 1.0.3 dated 2018-01-24

Title: Render Graphs Using 'Sigma.js'
Description: Create interactive graph visualizations using 'Sigma.js' <http://sigmajs.org/>. This package is meant to be used in conjunction with 'igraph', replacing the (somewhat underwhelming) plotting features of the package. The idea is to quickly render graphs, regardless of their size, in a way that allows for easy, iterative modification of aesthetics. Because 'Sigma.js' is a 'javascript' library, the visualizations are inherently interactive and are well suited for integration with 'Shiny' apps. While there are several 'htmlwidgets' focused on network visualization, they tend to underperform on medium to large sized graphs. 'Sigma.js' was designed for larger network visualizations and this package aims to make those strengths available to 'R' users.
Author: Ian Kloo [aut, cre]
Maintainer: Ian Kloo <iankloo@gmail.com>

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Package Morpho updated to version 2.6 with previous version 2.5.1 dated 2017-04-21

Title: Calculations and Visualisations Related to Geometric Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph], Gregory Jefferis [ctb], Dryden Ian [cph]
Maintainer: Stefan Schlager <zarquon42@gmail.com>

Diff between Morpho versions 2.5.1 dated 2017-04-21 and 2.6 dated 2018-04-23

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Package CorReg updated to version 1.2.8 with previous version 1.2.1 dated 2017-05-03

Title: Linear Regression Based on Linear Structure Between Variables
Description: Linear regression based on a recursive structural equation model (explicit multiples correlations) found by a M.C.M.C. algorithm. It permits to face highly correlated variables. Variable selection is included (by lasso, elastic net, etc.). It also provides some graphical tools for basic statistics.
Author: Clement THERY [aut, cre], Christophe BIERNACKI [ctb], Gaetan LORIDANT [ctb], Florian WATRIN [ctb], Quentin GRIMONPREZ [ctb], Vincent KUBICKI [ctb], Samuel BLANCK [ctb], Jeremie KELLNER [ctb]
Maintainer: Clement THERY <corregeous@correg.org>

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Package ohtadstats updated to version 1.1.0 with previous version 1.0 dated 2018-03-01

Title: Tomoka Ohta D Statistics
Description: Calculate's Tomoka Ohta's partitioning of linkage disequilibrium, deemed D-statistics, for pairs of loci. Beissinger et al. (2016) <doi:10.1038/hdy.2015.81>.
Author: Paul F. Petrowski <pfpetrowski@mail.missouri.edu> & Timothy M. Beissinger <timbeissinger@gmail.com>
Maintainer: Paul F. Petrowski <pfpetrowski@mail.missouri.edu>

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Package tactile updated to version 0.2.0 with previous version 0.1.0 dated 2017-11-15

Title: New and Extended Plots, Methods, and Panel Functions for 'lattice'
Description: Extensions to 'lattice', providing new high-level functions, methods for existing functions, panel functions, and a theme.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>), Deepayan Sarkar [ctb, cph] (lattice), Brian Ripley [ctb] (stats::plot.acf)
Maintainer: Johan Larsson <johanlarsson@outlook.com>

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Package orloca.es updated to version 4.5 with previous version 4.3 dated 2017-11-01

Title: Spanish version of orloca package
Description: Help and demo in Spanish of the orloca package. (Ayuda y demo en espanol del paquete orloca.) Objetos y metodos para manejar y resolver el problema de localizacion de suma minima, tambien conocido como problema de Fermat-Weber. El problema de localizacion de suma minima busca un punto tal que la suma ponderada de las distancias a los puntos de demanda se minimice. Vease "The Fermat-Weber location problem revisited" por Brimberg, Mathematical Programming, 1, pag. 71-76, 1995. <DOI: 10.1007/BF01592245>. Los algoritmos generales de optimizacion global se usan para resolver el problema, junto con el metodo adhoc Weiszfeld, ver "Sur le point pour lequel la Somme des distance de n points donnes est minimum", por Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pag. . 355-386, 1937.
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>

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Package fbati updated to version 1.0-3 with previous version 1.0-1.1 dated 2016-07-10

Title: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>

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Package nodiv updated to version 1.2.0 with previous version 1.1.9 dated 2018-03-13

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

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Package fold updated to version 0.2.6 with previous version 0.2.5 dated 2018-01-07

Title: A Self-Describing Dataset Format and Interface
Description: Defines a compact data format that includes metadata. The function fold() creates the format by converting from data.frame, and unfold() converts back. The predictability of the folded format supports reusability of data processing tools, while the presence of embedded metadata improves portability, interpretability, and efficiency.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package nmfem updated to version 1.0.2 with previous version 1.0.1 dated 2018-04-11

Title: NMF-EM Algorithm
Description: Provides a version of the Expectation-Maximization algorithm for mix-models, reducing the numbers of parameters to estimate using Non-negative Matrix Factorization methods. For more explanations, see pre-print of Carel and Alquier (2017) <arXiv:1709.03346>.
Author: Lena Carel [aut, cre]
Maintainer: Lena Carel <lena.carel@gmail.com>

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Package frailtyEM updated to version 0.8.7 with previous version 0.8.3 dated 2018-02-05

Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric baseline hazard with the Expectation-Maximization algorithm. Supported data formats include clustered failures with left truncation and recurrent events in gap-time or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable and the Power Variance Family are supported.
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <t.a.balan@lumc.nl>

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Package cubing updated to version 1.0-5 with previous version 1.0-4 dated 2018-04-14

Title: Rubik's Cube Solving
Description: Functions for visualizing, animating, solving and analyzing the Rubik's cube. Includes data structures for solvable and unsolvable cubes, random moves and random state scrambles and cubes, 3D displays and animations using 'OpenGL', patterned cube generation, and lightweight solvers. See Rokicki, T. (2008) <arXiv:0803.3435> for the Kociemba solver.
Author: Alec Stephenson.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>

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Package trtf updated to version 0.3-1 with previous version 0.3-0 dated 2018-01-08

Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with corresponding random forest for conditional transformation models as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>) and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package svGUI updated to version 1.0.0 with previous version 0.9-55 dated 2014-03-02

Title: SciViews - Manage GUIs in R
Description: The SciViews svGUI package eases the management of Graphical User Interfaces (GUI) in R. It is independent from any particular GUI widgets (Tk, Gtk2, native, ...). It centralizes info about GUI elements currently used, and it dispatches GUI calls to the particular toolkits in use in function of the context (is R run at the terminal, within a Tk application, a HTML page?).
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>

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Package RcppThread updated to version 0.2.0 with previous version 0.1.3 dated 2017-12-27

Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>

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Package multipanelfigure updated to version 1.0.0 with previous version 0.10.7 dated 2018-04-03

Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Description: Tools to create a layout for figures made of multiple panels, and to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap' plots, grobs, and PNG, JPEG, SVG and TIFF images.
Author: Johannes Graumann [cre, aut], Richard Cotton [ctb]
Maintainer: Johannes Graumann <johannes.graumann@mpi-bn.mpg.de>

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Package spBayesSurv updated to version 1.1.3 with previous version 1.1.2 dated 2018-01-11

Title: Bayesian Modeling and Analysis of Spatially Correlated Survival Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC).
Author: Haiming Zhou <zhouh@niu.edu> and Timothy Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>

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Package rpql updated to version 0.6 with previous version 0.5 dated 2016-10-07

Title: Regularized PQL for Joint Selection in GLMMs
Description: Performs joint selection in Generalized Linear Mixed Models (GLMMs) using penalized likelihood methods. Specifically, the Penalized Quasi-Likelihood (PQL) is used as a loss function, and penalties are then "added on" to perform simultaneous fixed and random effects selection. Regularized PQL avoids the need for integration (or approximations such as the Laplace's method) during the estimation process, and so the full solution path for model selection can be constructed relatively quickly.
Author: Francis K.C. Hui, Samuel Mueller, A.H. Welsh
Maintainer: Francis Hui <fhui28@gmail.com>

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Package missRanger updated to version 1.0.2 with previous version 1.0.1 dated 2018-03-22

Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest' algorithm used to impute mixed-type data sets by chaining tree ensembles, 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>

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Package grex updated to version 1.8 with previous version 1.7 dated 2017-11-05

Title: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Description: Convert 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>), Gao Wang [aut], Lei Sun [aut]
Maintainer: Nan Xiao <me@nanx.me>

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Package exampletestr updated to version 1.3.0 with previous version 1.2.0 dated 2018-01-26

Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions and use them to create shells (skeletons which must be manually completed by the user) of test files to be tested with the 'testthat' package.
Author: Rory Nolan [aut, cre], Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package tram updated to version 0.2-1 with previous version 0.2-0 dated 2018-02-26

Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package slam updated to version 0.1-43 with previous version 0.1-42 dated 2017-12-21

Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), David Meyer [aut], Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between slam versions 0.1-42 dated 2017-12-21 and 0.1-43 dated 2018-04-23

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Package relations updated to version 0.6-8 with previous version 0.6-7 dated 2017-08-09

Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Author: David Meyer [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between relations versions 0.6-7 dated 2017-08-09 and 0.6-8 dated 2018-04-23

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Package clue updated to version 0.3-55 with previous version 0.3-54 dated 2017-08-09

Title: Cluster Ensembles
Description: CLUster Ensembles.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Walter Böhm [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between clue versions 0.3-54 dated 2017-08-09 and 0.3-55 dated 2018-04-23

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Package dcurver updated to version 0.9.1 with previous version 0.9.0 dated 2018-04-05

Title: Utility Functions for Davidian Curves
Description: A Davidian curve defines a seminonparametric density, whose shape and flexibility can be tuned by easy to estimate parameters. Since a special case of a Davidian curve is the standard normal density, Davidian curves can be used for relaxing normality assumption in statistical applications (Zhang & Davidian, 2001) <doi:10.1111/j.0006-341X.2001.00795.x>. This package provides the density function, the gradient of the loglikelihood and a random generator for Davidian curves.
Author: Oğuzhan Öğreden
Maintainer: Oğuzhan Öğreden <oguzhan@oguzhanogreden.com>

Diff between dcurver versions 0.9.0 dated 2018-04-05 and 0.9.1 dated 2018-04-23

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Package ACTCD updated to version 1.2-0 with previous version 1.1-0 dated 2016-12-17

Title: Asymptotic Classification Theory for Cognitive Diagnosis
Description: Cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; <doi:10.1007/s11336-009-9125-0>). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.
Author: Chia-Yi Chiu (Rutgers, the State University of New Jersey) and Wenchao Ma (The University of Alabama)
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>

Diff between ACTCD versions 1.1-0 dated 2016-12-17 and 1.2-0 dated 2018-04-23

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Package APML0 updated to version 0.9 with previous version 0.8 dated 2018-04-15

Title: Augmented and Penalized Minimization Method L0
Description: Fit linear, logistic and Cox models regularized with L0, lasso (L1), elastic-net (L1 and L2), or net (L1 and Laplacian) penalty, and their adaptive forms, such as adaptive lasso / elastic-net and net adjusting for signs of linked coefficients. It solves L0 penalty problem by simultaneously selecting regularization parameters and the number of non-zero coefficients. This augmented and penalized minimization method provides an approximation solution to the L0 penalty problem, but runs as fast as L1 regularization problem. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients. It could deal with very high dimensional data and has superior selection performance.
Author: Xiang Li, Shanghong Xie, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li <xli256@its.jnj.com>

Diff between APML0 versions 0.8 dated 2018-04-15 and 0.9 dated 2018-04-23

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Sun, 22 Apr 2018

Package spatial.tools updated to version 1.6.0 with previous version 1.4.8 dated 2014-07-02

Title: R Functions for Working with Spatial Data
Description: Spatial functions meant to enhance the core functionality of the package "raster", including a parallel processing engine for use with rasters.
Author: Jonathan Asher Greenberg
Maintainer: Jonathan Asher Greenberg <spatial-tools@estarcion.net>

Diff between spatial.tools versions 1.4.8 dated 2014-07-02 and 1.6.0 dated 2018-04-22

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Package reportReg updated to version 0.2.0 with previous version 0.1.0 dated 2017-05-19

Title: An Easy Way to Report Regression Analysis
Description: Provides an easy way to report the results of regression analysis, including: 1. Proportional hazards regression model from function 'coxph' of package 'survival'; 2. Ordered logistic regression from function 'polr' of package 'MASS'; 3. Binary logistic regression from function 'glm' of package 'stats'; 4. Linear regression from function 'lm' of package 'stats'; 5. Risk regression model for survival analysis with competing risks from function 'FGR' of package 'riskRegression'; 6. Multilevel model from function 'lme' of package 'nlme'.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

Diff between reportReg versions 0.1.0 dated 2017-05-19 and 0.2.0 dated 2018-04-22

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Package gdalUtils updated to version 2.0.1.14 with previous version 2.0.1.7 dated 2015-10-10

Title: Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>

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Package disclapmix updated to version 1.7 with previous version 1.6.2 dated 2015-09-09

Title: Discrete Laplace Mixture Inference using the EM Algorithm
Description: Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Author: Mikkel Meyer Andersen [aut, cre], Poul Svante Eriksen [aut]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>

Diff between disclapmix versions 1.6.2 dated 2015-09-09 and 1.7 dated 2018-04-22

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Package compareGroups updated to version 3.3.4 with previous version 3.3.3 dated 2018-01-29

Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Hector Sanz, Gavin Lucas, Judith Penafiel and David Gimenez
Maintainer: Isaac Subirana <isubirana@imim.es>

Diff between compareGroups versions 3.3.3 dated 2018-01-29 and 3.3.4 dated 2018-04-22

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Package NITPicker updated to version 0.1.2 with previous version 0.1.1 dated 2018-04-20

Title: Finds the Best Subset of Points to Sample
Description: Given a few examples of experiments over a time (or spatial) course, 'NITPicker' selects a subset of points to sample in follow-up experiments, which would (i) best distinguish between the experimental conditions and the control condition (ii) best distinguish between two models of how the experimental condition might differ from the control (iii) a combination of the two. Ezer and Keir (2018) <doi:10.1101/301796>.
Author: Daphne Ezer
Maintainer: Daphne Ezer <dezer@turing.ac.uk>

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Package chorrrds updated to version 0.1.4 with previous version 0.1.3 dated 2018-04-19

Title: Music Chords Extraction
Description: Extracts music chords from the 'CifraClub' website <https://www.cifraclub.com.br/>. The package also has functions for cleaning the extracted data and feature extraction.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>

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Package RRPP updated to version 0.2.0 with previous version 0.1.0 dated 2018-01-22

Title: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure
Description: Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. This method is described by Collyer, Sekora, & Adams (2015) <doi:10.1038/hdy.2014.75>.
Author: Michael Collyer, Dean Adams
Maintainer: Michael Collyer <mlcollyer@gmail.com>

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Package clustermq updated to version 0.8.4 with previous version 0.8.3 dated 2018-01-21

Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers in single line of code. All processing is done on the network without accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert <mschu.dev@gmail.com>
Maintainer: Michael Schubert <mschu.dev@gmail.com>

Diff between clustermq versions 0.8.3 dated 2018-01-21 and 0.8.4 dated 2018-04-22

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Package Rnightlights updated to version 0.2.0 with previous version 0.1.5 dated 2018-01-07

Title: Satellite Nightlight Data Extraction
Description: Extracts raster and zonal statistics from satellite nightlight rasters downloaded from the United States National Oceanic and Atmospheric Administration (<http://www.noaa.gov>) free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly nightlight raster data are supported. Satellite nightlight raster tiles are downloaded and cropped to the country boundaries using shapefiles from the GADM database of Global Administrative Areas (<http://gadm.org>). Zonal statistics are then calculated at the lowest administrative boundary for the selected country and cached locally for future retrieval. Finally, a simple data explorer/browser is included that allows one to visualize the cached data e.g. graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph]
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>

Diff between Rnightlights versions 0.1.5 dated 2018-01-07 and 0.2.0 dated 2018-04-22

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Package rcube updated to version 0.2 with previous version 0.1 dated 2018-04-12

Title: Simulations and Visualizations of Rubik's Cube (with Mods)
Description: Provides simplified methods for managing classic Rubik's cubes and many other modifications of it (such as NxNxN size cubes, void cubes and 8-coloured cubes - so called octa cubes). Includes functions of handling special syntax for managing such cubes; and different approach to plotting 3D cubes without using external libraries (for example 'OpenGL').
Author: Wojciech Rosa
Maintainer: Wojciech Rosa <w.rosa@pollub.pl>

Diff between rcube versions 0.1 dated 2018-04-12 and 0.2 dated 2018-04-22

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Permanent link

Package SSDforR updated to version 1.4.18 with previous version 1.4.17 dated 2017-10-06

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

Diff between SSDforR versions 1.4.17 dated 2017-10-06 and 1.4.18 dated 2018-04-22

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Package psgp updated to version 0.3-18 with previous version 0.3-17 dated 2018-04-13

Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging (Ingram 'et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation (Barillec 'et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram <ingrambr@gmail.com>, Remi Barillec <remi@igiltd.com>, Jon Olav Skoien <jon.skoien@gmail.com>
Maintainer: Ben Ingram <ingrambr@gmail.com>

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Package ks updated to version 1.11.1 with previous version 1.11.0 dated 2018-01-16

Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Duong (2017) <doi:10.18637/jss.v021.i07>.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>

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Package GGIR updated to version 1.5-21 with previous version 1.5-18 dated 2018-03-18

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in van Hees and colleagues (2014) <doi: 10.1152/japplphysiol.00421.2014> and (2015) <doi: 10.1371/journal.pone.0142533>. The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <http://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com/product/ax3>. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb], Jairo H Migueles [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>

Diff between GGIR versions 1.5-18 dated 2018-03-18 and 1.5-21 dated 2018-04-22

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 GGIR-1.5-21/GGIR/R/g.part5.R                         |  317 +++++++---
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 GGIR-1.5-21/GGIR/R/identify_level.R                  |   30 -
 GGIR-1.5-21/GGIR/README.md                           |    2 
 GGIR-1.5-21/GGIR/build/vignette.rds                  |binary
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 GGIR-1.5-21/GGIR/man/GGIR-package.Rd                 |    4 
 GGIR-1.5-21/GGIR/man/g.part4.Rd                      |    4 
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 GGIR-1.5-21/GGIR/man/g.shell.GGIR.Rd                 |   10 
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 GGIR-1.5-21/GGIR/tests/testthat/test_chainof5parts.R |    7 
 GGIR-1.5-21/GGIR/vignettes/GGIR.Rmd                  |    5 
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 26 files changed, 611 insertions(+), 456 deletions(-)

More information about GGIR at CRAN
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Package VetResearchLMM updated to version 1.0.0 with previous version 0.2.0 dated 2017-04-04

Title: Linear Mixed Models - An Introduction with Applications in Veterinary Research
Description: R Codes and Datasets for Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998). Linear Mixed Models. An Introduction with applications in Veterinary Research. International Livestock Research Institute.
Author: Muhammad Yaseen [aut, cre], Luc Duchateau [ctb], Paul Janssen [ctb], John Rowlands [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>

Diff between VetResearchLMM versions 0.2.0 dated 2017-04-04 and 1.0.0 dated 2018-04-22

 DESCRIPTION         |   10 ++++---
 MD5                 |   30 +++++++++++------------
 NEWS.md             |    5 +++
 R/Examp2.5.2.1.R    |   17 ++++++-------
 R/Examp2.5.3.1.R    |   24 +++++++++---------
 R/Examp2.6.1.R      |   21 +++++++++-------
 R/Examp3.1.R        |   44 +++++++++++++++++-----------------
 R/Examp3.2.R        |   14 +++++------
 R/Examp3.3.R        |   66 ++++++++++++++++++++++++++--------------------------
 README.md           |    4 +--
 man/Examp2.5.2.1.Rd |   13 ++++------
 man/Examp2.5.3.1.Rd |   14 +++++------
 man/Examp2.6.1.Rd   |   19 ++++++++------
 man/Examp3.1.Rd     |   42 ++++++++++++++++-----------------
 man/Examp3.2.Rd     |   12 ++++-----
 man/Examp3.3.Rd     |   54 +++++++++++++++++++++---------------------
 16 files changed, 200 insertions(+), 189 deletions(-)

More information about VetResearchLMM at CRAN
Permanent link


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