Wed, 16 May 2018

Package YuGene updated to version 1.1.6 with previous version 1.1.5 dated 2015-11-19

Title: A Simple Approach to Scale Gene Expression Data Derived from Different Platforms for Integrated Analyses
Description: Simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart <f.rohart@uq.edu.au>

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Package VNM updated to version 7.1 with previous version 6.1 dated 2018-02-15

Title: Finding Multiple-Objective Optimal Designs for the 4-Parameter Logistic Model
Description: Provide tools for finding multiple-objective optimal designs for estimating the shape of dose-response, the ED50 (the dose producing an effect midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives. The acronym VNM stands for V-algorithm using Newton Raphson method to search multiple-objective optimal design.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang <yarongyang78@gmail.com>

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Package VineCopula updated to version 2.1.5 with previous version 2.1.4 dated 2018-02-11

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Thomas Nagler [aut, cre], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthias Killiches [ctb], Harry Joe [ctb], Thibault Vatter [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

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Package PreProcess updated to version 3.1.5 with previous version 3.1.4 dated 2017-07-13

Title: Basic Functions for Pre-Processing Microarrays
Description: Provides classes to pre-process microarray gene expression data as part of the OOMPA collection of packages described at <http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Package MLML2R updated to version 0.2.1 with previous version 0.2.0 dated 2018-02-21

Title: Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Description: Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2018, to appear).
Author: Samara Kiihl [aut, cre], Maria Jose Martinez-Garrido [aut], Arce Domingo-Relloso [aut], Jose Bermudez [aut], Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>

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Package bootsPLS updated to version 1.1.2 with previous version 1.1.1 dated 2017-12-17

Title: Bootstrap Subsamplings of Sparse Partial Least Squares - Discriminant Analysis for Classification and Signature Identification
Description: Applicable to any classification problem with more than 2 classes. It relies on bootstrap subsamplings of sPLS-DA and provides tools to select the most stable variables (defined as the ones consistently selected over the bootstrap subsamplings) and to predict the class of test samples.
Author: Florian Rohart [aut, cre], Kim-Anh Le Cao [boss], Christine Wells [boss]
Maintainer: Florian Rohart <florian.rohart@gmail.com>

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Package icsw updated to version 1.0.0 with previous version 0.9 dated 2015-07-07

Title: Inverse Compliance Score Weighting
Description: Provides the necessary tools to estimate average treatment effects with an instrumental variable by re-weighting observations using a model of compliance.
Author: Peter M. Aronow <peter.aronow@yale.edu>, Dean Eckles <icsw@deaneckles.com> and Kyle Peyton <kyle.peyton@yale.edu>
Maintainer: Kyle Peyton <kyle.peyton@yale.edu>

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Package RNOmni updated to version 0.4.0 with previous version 0.3.0 dated 2018-04-18

Title: Omnibus Test for Genetic Association Analysis using the Rank Normal Transformation
Description: Implementation of genetic association tests using the rank based inverse normal transformation (INT). The primary contribution is an omnibus test, which synthesizes two complementary INT-based approaches. In simulations against phenotypes with skewed and heavy tailed residuals, the omnibus test provided valid inference in the absence of genetic effects. When genetic effects were present, the omnibus test provided power comparable to the more efficient of the component methods. Under these settings, standard linear regression variously failed to control the type I error in the absence of genetic effects, and was underpowered in the presence of genetic effects.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>

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Package MPSEM updated to version 0.3-4 with previous version 0.3-3 dated 2017-09-25

Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>

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Package FSelector updated to version 0.31 with previous version 0.21 dated 2016-06-30

Title: Selecting Attributes
Description: Functions for selecting attributes from a given dataset. Attribute subset selection is the process of identifying and removing as much of the irrelevant and redundant information as possible.
Author: Piotr Romanski, Lars Kotthoff
Maintainer: Lars Kotthoff <larsko@uwyo.edu>

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Package eive updated to version 2.3 with previous version 2.1 dated 2014-07-05

Title: An Algorithm for Reducing Errors-in-Variable Bias in Simple Linear Regression
Description: Performs a compact genetic algorithm search to reduce errors-in-variables bias in linear regression. The algorithm estimates the regression parameters with lower biases and higher variances but mean-square errors (MSEs) are reduced.
Author: Mehmet Hakan Satman (PhD), Erkin Diyarbakirlioglu (PhD)
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>

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Package edci updated to version 1.1-3 with previous version 1.1-2 dated 2016-08-24

Title: Edge Detection and Clustering in Images
Description: Detection of edge points in images based on the difference of two asymmetric M-kernel estimators. Linear and circular regression clustering based on redescending M-estimators. Detection of linear edges in images.
Author: Tim Garlipp <TimGarlipp@gmx.de>
Maintainer: Dominik Kirchhoff <dominik.kirchhoff@tu-dortmund.de>

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Package rCBA updated to version 0.4.2 with previous version 0.4.1 dated 2018-05-09

Title: CBA Classifier for R
Description: Provides implementations of a classifier based on the "Classification Based on Associations" (CBA). It can be used for building classification models from association rules. Rules are pruned in the order of precedence given by the sort criteria and a default rule is added. The final classifier labels provided instances. CBA was originally proposed by Liu, B. Hsu, W. and Ma, Y. Integrating Classification and Association Rule Mining. Proceedings KDD-98, New York, 27-31 August. AAAI. pp80-86 (1998, ISBN:1-57735-070-7).
Author: Jaroslav Kuchar [aut, cre], Tomas Kliegr [ctb]
Maintainer: Jaroslav Kuchar <jaroslav.kuchar@gmail.com>

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Package FeaLect updated to version 1.12 with previous version 1.10 dated 2015-05-12

Title: Scores Features for Feature Selection
Description: For each feature, a score is computed that can be useful for feature selection. Several random subsets are sampled from the input data and for each random subset, various linear models are fitted using lars method. A score is assigned to each feature based on the tendency of LASSO in including that feature in the models.Finally, the average score and the models are returned as the output. The features with relatively low scores are recommended to be ignored because they can lead to overfitting of the model to the training data. Moreover, for each random subset, the best set of features in terms of global error is returned. They are useful for applying Bolasso, the alternative feature selection method that recommends the intersection of features subsets.
Author: Habil Zare
Maintainer: Habil Zare <zare@txstate.edu>

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Package codep updated to version 0.9-1 with previous version 0.8-1 dated 2018-04-16

Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional feature.
Author: Guillaume Guenard and Pierre Legendre, Bertrand Pages
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>

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Package astrochron updated to version 0.8 with previous version 0.7 dated 2017-06-14

Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers [aut,cre], Alberto Malinverno [ctb], Linda Hinnov [ctb], Vincent Moron [ctb]
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>

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Package PowerUpR updated to version 1.0.0 with previous version 0.2.3 dated 2018-02-16

Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: R version of PowerUp! <https://www.causalevaluation.org/>. Includes tools to calculate statistical power, minimum detectable effect size, and minimum required sample size for various multilevel randomized experiments with continuous outcomes.
Author: Metin Bulus [aut, cre, trl], Nianbo Dong [aut], Benjamin Kelcey [aut], Jessaca Spybrook [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

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Package RECA updated to version 1.6 with previous version 1.5 dated 2018-04-20

Title: Relevant Component Analysis for Supervised Distance Metric Learning
Description: Relevant Component Analysis (RCA) tries to find a linear transformation of the feature space such that the effect of irrelevant variability is reduced in the transformed space.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>)
Maintainer: Nan Xiao <me@nanx.me>

Diff between RECA versions 1.5 dated 2018-04-20 and 1.6 dated 2018-05-16

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Package InSilicoVA updated to version 1.2.0 with previous version 1.1.5 dated 2017-11-19

Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>

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Package biogas updated to version 1.10.3 with previous version 1.10.2 dated 2018-05-02

Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Biogas quantity and composition can be predicted from substrate composition and additional, optional data. Lastly, inoculum and substrate mass can be determined for planning BMP experiments.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@eng.au.dk>

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Package spgs updated to version 1.0-2 with previous version 1.0-1 dated 2017-07-21

Title: Statistical Patterns in Genomic Sequences
Description: A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
Author: Andrew Hart [aut, cre], Servet Martínez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
Maintainer: Andrew Hart <ahart@dim.uchile.cl>

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Package skpr updated to version 0.49.0 with previous version 0.47.5 dated 2018-03-26

Title: Design of Experiments Suite: Generate and Evaluate Optimal Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre], George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

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Package repo updated to version 2.1.3 with previous version 2.1.2 dated 2017-11-27

Title: A Data-Centered Data Flow Manager
Description: A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with rich annotations, including corresponding code chunks, and easily searched and retrieved.
Author: Francesco Napolitano <franapoli@gmail.com>
Maintainer: Francesco Napolitano <franapoli@gmail.com>

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Package RcmdrPlugin.MPAStats updated to version 1.2.2 with previous version 1.2.1 dated 2016-05-13

Title: R Commander Plug-in for MPA Statistics
Description: Extends R Commander with a unified menu of new and pre-existing statistical functions related to public management and policy analysis statistics. Functions and menus have been renamed according to the usage in PMGT 630 in the Master of Public Administration program at Brigham Young University.
Author: Andrew Heiss, Richard Payne, Christa Schank, Jessica Reese
Maintainer: Andrew Heiss <andrew@andrewheiss.com>

Diff between RcmdrPlugin.MPAStats versions 1.2.1 dated 2016-05-13 and 1.2.2 dated 2018-05-16

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Package openVA updated to version 1.0.4 with previous version 1.0.3 dated 2017-01-07

Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>

Diff between openVA versions 1.0.3 dated 2017-01-07 and 1.0.4 dated 2018-05-16

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Package mmeln updated to version 1.3 with previous version 1.2 dated 2015-09-25

Title: Estimation of Multinormal Mixture Distribution
Description: Fit multivariate mixture of normal distribution using covariance structure.
Author: Charles-Edouard Giguere
Maintainer: Charles-Edouard Giguere <ce.giguere@gmail.com>

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Package timedelay updated to version 1.0.8 with previous version 1.0.7 dated 2017-05-27

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

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Package spartan updated to version 3.0.1 with previous version 3.0.0 dated 2017-09-06

Title: Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. 'spartan', first described in our 2013 publication in PLoS Computational Biology, provided code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 added support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions. Version 3.0 offers significant additional functionality that permits the creation of emulations of simulation results, derived using the same sampling techniques in the global sensitivity analysis techniques, and the generation of combinations of these machine learning algorithms to one create one predictive tool, more commonly known as an ensemble model. Version 3.0 also improved the standard of the graphs produced in the original sensitivity analysis techniques, and introduced a polar plot to examine parameter sensitivity.
Author: Kieran Alden [cre, aut], Mark Read [aut], Paul Andrews [aut], Jason Cosgrove [aut], Mark Coles [aut], Jon Timmis [aut]
Maintainer: Kieran Alden <kieran.alden@gmail.com>

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More information about spartan at CRAN
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Package popEpi updated to version 0.4.5 with previous version 0.4.4 dated 2017-11-14

Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models, rates, mean survival times, relative survival, and standardized incidence and mortality ratios (SIRs/SMRs), all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.
Author: Joonas Miettinen [aut, cre], Matti Rantanen [aut], Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>

Diff between popEpi versions 0.4.4 dated 2017-11-14 and 0.4.5 dated 2018-05-16

 popEpi-0.4.4/popEpi/tests/testthat/test_splitting_randomly.R                |only
 popEpi-0.4.5/popEpi/DESCRIPTION                                             |   20 
 popEpi-0.4.5/popEpi/MD5                                                     |  264 
 popEpi-0.4.5/popEpi/NAMESPACE                                               |  176 
 popEpi-0.4.5/popEpi/NEWS.md                                                 |  274 
 popEpi-0.4.5/popEpi/R/S3_definitions.R                                      | 2946 +++++-----
 popEpi-0.4.5/popEpi/R/aggregating.R                                         | 1232 ++--
 popEpi-0.4.5/popEpi/R/data_document.R                                       |  348 -
 popEpi-0.4.5/popEpi/R/direct_adjusting.R                                    |  314 -
 popEpi-0.4.5/popEpi/R/evaluation.R                                          | 1914 +++---
 popEpi-0.4.5/popEpi/R/flexyargs.R                                           |  332 -
 popEpi-0.4.5/popEpi/R/fractional_years.R                                    |  300 -
 popEpi-0.4.5/popEpi/R/incidence_rates.R                                     |  689 +-
 popEpi-0.4.5/popEpi/R/incidence_rates_utils.R                               |  266 
 popEpi-0.4.5/popEpi/R/lexpand.R                                             | 1880 +++---
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Package NSM3 updated to version 1.12 with previous version 1.11 dated 2018-02-25

Title: Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider <schneider.393@osu.edu>

Diff between NSM3 versions 1.11 dated 2018-02-25 and 1.12 dated 2018-05-16

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 3 files changed, 5 insertions(+), 6 deletions(-)

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Package getTBinR updated to version 0.5.4 with previous version 0.5.3 dated 2018-03-10

Title: Get WHO Tuberculosis Data
Description: Facilitates easy import of analysis ready World Health Organisation Tuberculosis data and provides plotting functions for exploratory data analysis.
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>)
Maintainer: Sam Abbott <contact@samabbott.co.uk>

Diff between getTBinR versions 0.5.3 dated 2018-03-10 and 0.5.4 dated 2018-05-16

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New package furrr with initial version 0.1.0
Package: furrr
Version: 0.1.0
Title: Apply Mapping Functions in Parallel using Futures
Depends: R (>= 3.2.0), future (>= 1.6.2)
Imports: globals (>= 0.10.3), rlang (>= 0.2.0), purrr (>= 0.2.4)
Suggests: listenv (>= 0.6.0), dplyr (>= 0.7.4), testthat
Authors@R: c( person("Davis", "Vaughan", email = "dvaughan@business-science.io", role = c("aut", "cre")), person("Matt", "Dancho", email = "mdancho@business-science.io", role = c("aut")) )
Maintainer: Davis Vaughan <dvaughan@business-science.io>
Description: Implementations of the family of map() functions from 'purrr' that can be resolved using any 'future'-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.
License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/DavisVaughan/furrr
BugReports: https://github.com/DavisVaughan/furrr/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-14 19:53:18 UTC; davisvaughan
Author: Davis Vaughan [aut, cre], Matt Dancho [aut]
Repository: CRAN
Date/Publication: 2018-05-16 16:04:29 UTC

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Package crackR (with last version 0.3-9) was removed from CRAN

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

2014-04-22 0.3-9

Permanent link
Package VideoComparison (with last version 0.15) was removed from CRAN

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

2015-07-25 0.15
2014-07-09 0.11
2013-12-10 0.9-4

Permanent link
New package zeitgebr with initial version 0.3.1
Package: zeitgebr
Title: Analysis of Circadian Behaviours
Date: 2018-05-15
Version: 0.3.1
Authors@R: c( person("Quentin", "Geissmann", role = c("aut", "cre"), email = "qgeissmann@gmail.com"), person("Luis", "Garcia", role = c("aut"), email = "luis.garcia@uni-muenster.de") )
Description: Use behavioural variables to compute period, rhythmicity and other circadian parameters. Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>), Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>), and autocorrelation-based periodograms.
Depends: R (>= 3.00), behavr
Imports: data.table, lomb, ggplot2, pracma
Suggests: testthat, covr, knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/rethomics/zeitgebr
BugReports: https://github.com/rethomics/zeitgebr/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-16 11:11:00 UTC; quentin
Author: Quentin Geissmann [aut, cre], Luis Garcia [aut]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Repository: CRAN
Date/Publication: 2018-05-16 15:36:48 UTC

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New package SemNetCleaner with initial version 0.1.1
Package: SemNetCleaner
Title: An Automated Cleaning Tool for Semantic and Linguistic Data
Version: 0.1.1
Date: 2018-05-11
Author: Alexander Christensen
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Description: Implements several functions that automatize the cleaning, removal of plurals and continuous strings, making the data binary, converging, and finalizing of linguistic data for semantic network analysis. Also provides a partial bootstrapped network function and plot.
Depends: R (>= 3.3.0)
License: GPL (>= 3.0)
Encoding: UTF-8
LazyData: true
Imports: qdap, tm, foreach, parallel, doParallel, NetworkToolbox, ggplot2, dplyr, plyr, RColorBrewer, purrr, magrittr, grid
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2018-05-15 20:10:08 UTC; APCHRIST
Repository: CRAN
Date/Publication: 2018-05-16 15:15:15 UTC

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Package sdcMicro updated to version 5.3.0 with previous version 5.2.0 dated 2018-04-13

Title: Statistical Disclosure Control Methods for Anonymization of Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly confidential. This package can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. In addition, various risk estimation methods are included. Note that the package includes a graphical user interface that allows to use various methods of this package.
Author: Matthias Templ [aut, cre], Bernhard Meindl [aut], Alexander Kowarik [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between sdcMicro versions 5.2.0 dated 2018-04-13 and 5.3.0 dated 2018-05-16

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Package netgwas updated to version 1.5.0 with previous version 0.1.4.2 dated 2018-04-06

Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <arXiv:1710.00894> and Behrouzi and Wit (2017) <arXiv:1710.01063>. NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>

Diff between netgwas versions 0.1.4.2 dated 2018-04-06 and 1.5.0 dated 2018-05-16

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 4 files changed, 66 insertions(+), 53 deletions(-)

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New package microsynth with initial version 1.0.9
Package: microsynth
Title: Synthetic Control Methods with Micro- And Meso-Level Data
Version: 1.0.9
Description: A generalization of the 'Synth' package that is designed for data at a more granular level (e.g., micro-level). Provides functions to construct weights (including propensity score-type weights) and run analyses for synthetic control methods with micro- and meso-level data; see Robbins, Saunders, and Kilmer (2017) <doi:10.1080/01621459.2016.1213634>.
Depends: R (>= 3.3.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: boot, survey, MASS, stats, utils, kernlab, LowRankQP, nleqslv, pracma
Suggests: knitr, xlsx, rmarkdown
RoxygenNote: 6.0.1
Authors@R: c( person("Michael", "Robbins", , "mrobbins@rand.org", c("aut", "cre")), person("Steven", "Davenport", , "sdavenpo@rand.org", "aut"))
VignetteBuilder: knitr
NeedsCompilation: no
Author: Michael Robbins [aut, cre], Steven Davenport [aut]
Maintainer: Michael Robbins <mrobbins@rand.org>
URL: https://github.com/ssdavenport/microsynth
Packaged: 2018-05-15 19:12:47 UTC; sdavenpo
Repository: CRAN
Date/Publication: 2018-05-16 15:33:56 UTC

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New package insect with initial version 1.0.0
Package: insect
Type: Package
Title: Informatic Sequence Classification Trees
Version: 1.0.0
Authors@R: person("Shaun", "Wilkinson", email = "shaunpwilkinson@gmail.com", role = c("aut", "cre"))
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Description: Provides a bioinformatics pipeline for DNA meta-barcoding analysis, including functions for sequence parsing, demultiplexing, quality filtering and probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
License: GPL-3
LazyData: TRUE
URL: http://github.com/shaunpwilkinson/insect
BugReports: http://github.com/shaunpwilkinson/insect/issues
Encoding: UTF-8
Imports: ape (>= 3.0.0), aphid (>= 1.1.0), kmer (>= 1.0.1), openssl, phylogram (>= 2.0.0), stats, utils, xml2
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-16 13:28:14 UTC; shaun
Repository: CRAN
Date/Publication: 2018-05-16 16:00:04 UTC

More information about insect at CRAN
Permanent link

Package EdSurvey updated to version 2.0.3 with previous version 1.0.6 dated 2017-05-04

Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analysis functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/> including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: OECD <http://www.oecd.org/>, including PISA, TALIS, PIAAC; and IEA <http://www.iea.nl/>, including TIMSS, TIMSS Advanced, PIRLS, ICCS, ICILS, and CivEd.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>

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Package ctmm updated to version 0.5.0 with previous version 0.4.1 dated 2017-08-30

Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese & Fleming (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in Fleming et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, PĂ©ron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>, PĂ©ron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, and Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>

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New package SurvGSD with initial version 1.0.0
Package: SurvGSD
Type: Package
Title: Group Sequential Design for a Clinical Trial with Censored Survival Data
Version: 1.0.0
Depends: R (>= 3.1.0)
Imports: flexsurv, ldbounds, mnormt, stats
Author: Hsu, Chih-Yuan and Chen, Chen-Hsin
Maintainer: Chih-Yuan Hsu <cyhsu@stat.sinica.edu.tw>
Description: Sample size calculation utilizing the information fraction and the alpha spending function in a group sequential clinical trial with censored survival data from underlying generalized gamma survival distributions or log-logistic survival distributions. Hsu, C.-H., Chen, C.-H, Hsu, K.-N. and Lu, Y.-H. (2018) A useful design utilizing the information fraction in a group sequential clinical trial with censored survival data. To appear in Biometrics.
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-15 01:05:22 UTC; yhchen
Repository: CRAN
Date/Publication: 2018-05-16 14:09:03 UTC

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New package SK with initial version 1.1
Package: SK
Type: Package
Title: Segment-Based Ordinary Kriging and Segment-Based Regression Kriging for Spatial Prediction
Date: 2018-05-10
Version: 1.1
Authors@R: person("Yongze Song", email = "yongze.song@postgrad.curtin.edu.au", comment = c(ORCID = "0000-0003-3420-9622"), role = c("aut", "cre"))
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>
Description: Segment-based Kriging methods, including segment-based ordinary Kriging (SOK) and segment-based regression Kriging (SRK) for spatial prediction of line segment spatial data as described in Yongze Song (2018) <doi:10.1109/TITS.2018.2805817>. Includes the spatial prediction and spatial visualisation. The descriptions of the methods and case datasets refer to the citation information below.
Imports: stats, graphics, rgeos, RColorBrewer, sp, GD, rtop, FitAR, MASS
Depends: R (>= 3.4.0)
License: GPL-2
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-15 03:37:26 UTC; zack
Author: Yongze Song [aut, cre] (<https://orcid.org/0000-0003-3420-9622>)
Repository: CRAN
Date/Publication: 2018-05-16 14:17:01 UTC

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New package renpow with initial version 0.1-1
Package: renpow
Type: Package
Title: Renewable Power Systems and the Environment
Version: 0.1-1
Date: 2018-05-09
Author: Miguel F. Acevedo
Maintainer: Miguel F. Acevedo <acevedo@unt.edu>
Description: Supports calculations and visualization for renewable power systems and the environment. Analysis and graphical tools for DC and AC circuits and their use in electric power systems. Analysis and graphical tools for thermodynamic cycles and heat engines, supporting efficiency calculations in coal-fired power plants, gas-fired power plants. Calculations of carbon emissions and atmospheric CO2 dynamics. Analysis of power flow and demand for the grid, as well as power models for microgrids and off-grid systems. Provides resource and power generation for hydro power, wind power, and solar power.
License: GPL (>= 2)
URL: https://www.r-project.org/
LazyData: true
NeedsCompilation: no
Packaged: 2018-05-14 22:37:46 UTC; acevedo
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-05-16 14:01:38 UTC

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New package kdist with initial version 0.2
Package: kdist
Title: K-Distribution and Weibull Paper
Version: 0.2
Authors@R: person("Tim", "Lamont-Smith", email = "t.lamontsmith@gmail.com", role = c("aut", "cre"))
Maintainer: Tim Lamont-Smith <t.lamontsmith@gmail.com>
Author: Tim Lamont-Smith [aut, cre]
Description: Density, distribution function, quantile function and random generation for the K-distribution. A plotting function that plots data on Weibull paper and another function to draw additional lines. See results from package in T Lamont-Smith (2018), submitted J. R. Stat. Soc.
Depends: R (>= 3.1.1)
Imports: stats, graphics
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Packaged: 2018-05-14 17:21:00 UTC; Tim
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-05-16 14:22:02 UTC

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Package shadow updated to version 0.5.3 with previous version 0.5.0 dated 2018-03-06

Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre], Evyatar Erell [ctb], Itai Kloog [ctb], Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between shadow versions 0.5.0 dated 2018-03-06 and 0.5.3 dated 2018-05-16

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Package quantregGrowth updated to version 0.4-1 with previous version 0.4-0 dated 2018-03-06

Title: Growth Charts via Regression Quantiles
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms via B-splines with L1-norm difference penalties. See Muggeo, Sciandra, Tomasello and Calvo (2013) <doi:10.1007/s10651-012-0232-1> and <doi:10.13140/RG.2.2.12924.85122> for some code example.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>

Diff between quantregGrowth versions 0.4-0 dated 2018-03-06 and 0.4-1 dated 2018-05-16

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Package poibin updated to version 1.3 with previous version 1.2 dated 2013-02-14

Title: The Poisson Binomial Distribution
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution.
Author: Yili Hong
Maintainer: Yili Hong <yilihong@vt.edu>

Diff between poibin versions 1.2 dated 2013-02-14 and 1.3 dated 2018-05-16

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New package freegroup with initial version 1.0
Package: freegroup
Type: Package
Title: The Free Group
Version: 1.0
Date: 2018-05-07
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Depends: magrittr,methods
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Description: Provides functionality for manipulating elements of the free group (juxtaposition is represented by a plus) including inversion, multiplication by a scalar, group-theoretic power operation, and Tietze forms. The package is fully vectorized.
License: GPL-2
URL: https://github.com/RobinHankin/freegroup.git
BugReports: https://github.com/RobinHankin/freegroup/issues
NeedsCompilation: no
Packaged: 2018-05-14 19:47:51 UTC; rhankin
Repository: CRAN
Date/Publication: 2018-05-16 13:58:36 UTC

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Package congressbr updated to version 0.1.2 with previous version 0.1.1 dated 2017-06-20

Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/> respectively.
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>

Diff between congressbr versions 0.1.1 dated 2017-06-20 and 0.1.2 dated 2018-05-16

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Package tkrgl updated to version 0.8 with previous version 0.7 dated 2011-11-27

Title: 'TK' Widget Tools for 'rgl'
Description: Provides 'TK' widget tools for the 'rgl' package.
Author: Duncan Murdoch/Ming Chen
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

Diff between tkrgl versions 0.7 dated 2011-11-27 and 0.8 dated 2018-05-16

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Package NipponMap updated to version 0.2 with previous version 0.1 dated 2017-11-29

Title: Japanese Map Data and Functions
Description: Digital map data of Japan for choropleth mapping, including a circle cartogram.
Author: Susumu Tanimura [aut, cre]
Maintainer: Susumu Tanimura <aruminat@gmail.com>

Diff between NipponMap versions 0.1 dated 2017-11-29 and 0.2 dated 2018-05-16

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Package Nippon updated to version 0.7.1 with previous version 0.7 dated 2018-05-06

Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com> [aut, cre], Hironobu Takahashi [cph], Hajime Baba [cph], Takatsugu Nokubi [cph]
Maintainer: Susumu Tanimura <aruminat@gmail.com>

Diff between Nippon versions 0.7 dated 2018-05-06 and 0.7.1 dated 2018-05-16

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Package fst updated to version 0.8.6 with previous version 0.8.4 dated 2018-01-25

Title: Lightning Fast Serialization of Data Frames for R
Description: Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD compression library is owned by Facebook Inc.
Author: Mark Klik [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is author of the bundled LZ4 and ZSTD code and copyright holder of LZ4), Facebook, Inc. [cph] (Bundled ZSTD code)
Maintainer: Mark Klik <markklik@gmail.com>

Diff between fst versions 0.8.4 dated 2018-01-25 and 0.8.6 dated 2018-05-16

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Package BiDimRegression updated to version 2.0.0 with previous version 1.0.6 dated 2014-03-22

Title: Calculates the Bidimensional Regression Between Two 2D Configurations
Description: Calculates the bidimensional regression between two 2D configurations following the approach by Tobler (1965).
Author: Claus-Christian Carbon [aut], Alexander (Sasha) Pastukhov [cre, ctb]
Maintainer: Alexander (Sasha) Pastukhov <pastukhov.alexander@gmail.com>

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New package rust with initial version 1.3.5
Package: rust
Type: Package
Title: Ratio-of-Uniforms Simulation with Transformation
Version: 1.3.5
Date: 2018-05-16
Authors@R: person(c("Paul", "J."), "Northrop", email = "p.northrop@ucl.ac.uk", role = c("aut", "cre", "cph"))
Description: Uses the generalized ratio-of-uniforms (RU) method to simulate from univariate and (low-dimensional) multivariate continuous distributions. The user specifies the log-density, up to an additive constant. The RU algorithm is applied after relocation of mode of the density to zero, and the user can choose a tuning parameter r. For details see Wakefield, Gelfand and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random variates via the ratio-of-uniforms method, Statistics and Computing (1991) 1, 129-133. A Box-Cox variable transformation can be used to make the input density suitable for the RU method and to improve efficiency. In the multivariate case rotation of axes can also be used to improve efficiency. From version 1.2.0 the 'Rcpp' package <https://cran.r-project.org/package=Rcpp> can be used to improve efficiency.
Imports: graphics, methods, Rcpp (>= 0.12.10), spatstat, stats
License: GPL (>= 2)
LazyData: TRUE
Depends: R (>= 3.3.0)
RoxygenNote: 6.0.1
Suggests: bang, inline, knitr, microbenchmark, revdbayes, rmarkdown, testthat
VignetteBuilder: knitr
URL: http://github.com/paulnorthrop/rust
BugReports: http://github.com/paulnorthrop/rust/issues
LinkingTo: Rcpp (>= 0.12.10), RcppArmadillo
NeedsCompilation: yes
Packaged: 2018-05-16 09:07:16 UTC; paul
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2018-05-16 10:00:53 UTC

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Package mvSLOUCH updated to version 1.3.4 with previous version 1.3.3 dated 2017-06-18

Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>

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Package GLSME updated to version 1.0.4 with previous version 1.0.3 dated 2015-07-20

Title: Generalized Least Squares with Measurement Error
Description: Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>

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Package MM updated to version 1.6-5 with previous version 1.6-2 dated 2013-01-21

Title: The Multiplicative Multinomial Distribution
Description: Various utilities for the Multiplicative Multinomial distribution.
Author: Robin K. S. Hankin and P. M. E. Altham
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package rust (with last version 1.3.4) was removed from CRAN

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

2017-12-22 1.3.4
2017-12-17 1.3.3
2017-08-28 1.2.3
2017-06-01 1.2.1
2017-06-01 1.2.2
2017-05-27 1.2.0
2016-11-18 1.1.0
2016-10-10 1.0.0

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Package TFMPvalue updated to version 0.0.8 with previous version 0.0.6 dated 2015-11-29

Title: Efficient and Accurate P-Value Computation for Position Weight Matrices
Description: In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007) <DOI:10.1186/1748-7188-2-15>.
Author: Ge Tan <ge_tan@live.com>
Maintainer: Ge Tan <ge_tan@live.com>

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Package BGGE updated to version 0.6.3 with previous version 0.6.2 dated 2018-05-10

Title: Bayesian Genomic Linear Models Applied to GE Genome Selection
Description: Application of genome prediction for a continuous variable, focused on genotype by environment (GE) genomic selection models (GS). It consists a group of functions that help to create regression kernels for some GE genomic models proposed by JarquĂ­n et al. (2014) <doi:10.1007/s00122-013-2243-1> and Lopez-Cruz et al. (2015) <doi:10.1534/g3.114.016097>. Also, it computes genomic predictions based on Bayesian approaches. The prediction function uses an orthogonal transformation of the data and specific priors present by Cuevas et al. (2014) <doi:10.1534/g3.114.013094>.
Author: Italo Granato [aut, cre], Luna-Vázquez Francisco J. [aut], Cuevas Jaime [aut]
Maintainer: Italo Granato <italo.granato@gmail.com>

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Package xgboost updated to version 0.71.1 with previous version 0.6.4.1 dated 2018-01-23

Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.
Author: Tianqi Chen [aut], Tong He [aut, cre], Michael Benesty [aut], Vadim Khotilovich [aut], Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>), Hyunsu Cho [aut], Kailong Chen [aut], Rory Mitchell [aut], Ignacio Cano [aut], Tianyi Zhou [aut], Mu Li [aut], Junyuan Xie [aut], Min Lin [aut], Yifeng Geng [aut], Yutian Li [aut], XGBoost contributors [cph] (base XGBoost implementation)
Maintainer: Tong He <hetong007@gmail.com>

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Package sharpr2 updated to version 1.1.1.0 with previous version 1.0.0.0 dated 2017-11-07

Title: Estimating Regulatory Scores and Identifying ATAC-STARR Data
Description: An algorithm for identifying high-resolution driver elements for datasets from a high-definition reporter assay library. Xinchen Wang, Liang He, Sarah Goggin, Alham Saadat, Li Wang, Melina Claussnitzer, Manolis Kellis (2017) <doi:10.1101/193136>.
Author: Liang He
Maintainer: Liang He <lianghe@mit.edu>

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Package polyclip updated to version 1.8-7 with previous version 1.8-3 dated 2018-05-11

Title: Polygon Clipping
Description: R port of Angus Johnson's open source library Clipper. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.
Author: Angus Johnson [aut] (C++ original, http://www.angusj.com/delphi/clipper.php), Adrian Baddeley [aut, trl, cre], Brian D. Ripley [ctb], Elliott Sales de Andrade [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package MSGARCH updated to version 2.3 with previous version 2.1 dated 2018-02-26

Title: Markov-Switching GARCH Models
Description: Fit (by Maximum Likelihood or MCMC/Bayesian), simulate, and forecast various Markov-Switching GARCH models as described in Ardia et al. (2017) <https://ssrn.com/abstract=2845809>.
Author: David Ardia [aut], Keven Bluteau [aut, cre], Kris Boudt [ctb], Leopoldo Catania [aut], Alexios Ghalanos [ctb], Brian Peterson [ctb], Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>

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Package ChoR updated to version 0.0-4 with previous version 0.0-3 dated 2017-10-12

Title: Chordalysis R Package
Description: Learning the structure of graphical models from datasets with thousands of variables. More information about the research papers detailing the theory behind Chordalysis is available at <http://www.francois-petitjean.com/Research> (KDD 2016, SDM 2015, ICDM 2014, ICDM 2013). The R package development site is <https://github.com/HerrmannM/Monash-ChoR>.
Author: François Petitjean [aut], Matthieu Herrmann [aut, com, cre], Christoph Bergmeir [ctb]
Maintainer: Matthieu Herrmann <matthieu.herrmann@monash.edu>

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Package iemisc updated to version 0.9.7 with previous version 0.9.6 dated 2016-10-17

Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions (Engineering Economics, Civil & Environmental/Water Resources Engineering, Geometry, Statistics, GNU Octave length functions, Trigonometric functions in degrees, etc.).
Author: Irucka Embry [aut, cre], Felix Andrews [aut, ctb] (zoo code), Hans Werner Borchers [aut, ctb] (pracma code), Samit Basu [aut, ctb] (FreeMat code), David Bateman [aut, ctb] (GNU Octave code), Rik Wehbring [aut, ctb] (GNU Octave code)
Maintainer: Irucka Embry <iembry@ecoccs.com>

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Package datasus updated to version 0.4.1 with previous version 0.4.0 dated 2017-07-25

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 'EstatĂ­sticas Vitais'.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>

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Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.