Thu, 08 Feb 2018

Package vote updated to version 1.1-0 with previous version 1.0-0 dated 2017-02-20

Title: Election Vote Counting
Description: Counting election votes and determining election results by different methods, including the single transferable vote, approval, score and plurality methods.
Author: Hana Sevcikova, Bernard Silverman, Adrian Raftery
Maintainer: Hana Sevcikova<hanas@uw.edu>

Diff between vote versions 1.0-0 dated 2017-02-20 and 1.1-0 dated 2018-02-08

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Package evmix updated to version 2.9 with previous version 2.8 dated 2018-01-31

Title: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models are provided. Kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the 'evd' package is provided, so that users can safely interchange most code.
Author: Carl Scarrott, Yang Hu and Alfadino Akbar, University of Canterbury
Maintainer: Carl Scarrott <carl.scarrott@canterbury.ac.nz>

Diff between evmix versions 2.8 dated 2018-01-31 and 2.9 dated 2018-02-08

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Package wpp2017 updated to version 1.1-2 with previous version 1.1-1 dated 2017-09-30

Title: World Population Prospects 2017
Description: Provides data from the United Nation's World Population Prospects 2017.
Author: United Nations Population Division
Maintainer: Hana Sevcikova <hanas@uw.edu>

Diff between wpp2017 versions 1.1-1 dated 2017-09-30 and 1.1-2 dated 2018-02-08

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Package vegtable updated to version 0.1.1 with previous version 0.1.0 dated 2017-08-08

Title: Handling Vegetation Data Sets
Description: Import and handling data from vegetation-plot databases, especially data stored in 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg>). Also import/export routines for exchange of data with 'Juice' (<http://www.sci.muni.cz/botany/juice>) are implemented.
Author: Miguel Alvarez <kamapu78@gmail.com>
Maintainer: Miguel Alvarez <kamapu78@gmail.com>

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Package mvoutlier updated to version 2.0.9 with previous version 2.0.8 dated 2017-01-16

Title: Multivariate Outlier Detection Based on Robust Methods
Description: Various Methods for Multivariate Outlier Detection.
Author: Peter Filzmoser <P.Filzmoser@tuwien.ac.at> and Moritz Gschwandtner <e0125439@student.tuwien.ac.at>
Maintainer: P. Filzmoser <P.Filzmoser@tuwien.ac.at>

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Package BIGDAWG updated to version 2.1 with previous version 1.16 dated 2017-09-06

Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>

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Package BART updated to version 1.5 with previous version 1.4 dated 2018-02-04

Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut], Rodney Sparapani [aut, cre], Robert Gramacy [aut], Charles Spanbauer [aut], Matthew Pratola [aut], Jean-Sebastien Roy [ctb], Makoto Matsumoto [ctb], Takuji Nishimura [ctb], Bill Venables [ctb], Brian Ripley [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>

Diff between BART versions 1.4 dated 2018-02-04 and 1.5 dated 2018-02-08

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Package Rlabkey updated to version 2.2.0 with previous version 2.1.136 dated 2017-10-16

Title: Data Exchange Between R and LabKey Server
Description: The LabKey client library for R makes it easy for R users to load live data from a LabKey Server, <http://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a LabKey Server, provided they have appropriate permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

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Package fdadensity updated to version 0.1.1 with previous version 0.1.0 dated 2017-10-16

Title: Functional Data Analysis for Density Functions by Transformation to a Hilbert Space
Description: An implementation of the methodology described in Petersen and Mueller (2016) <doi:10.1214/15-AOS1363> for the functional data analysis of samples of density functions. Densities are first transformed to their corresponding log quantile densities, followed by ordinary Functional Principal Components Analysis (FPCA). Transformation modes of variation yield improved interpretation of the variability in the data as compared to FPCA on the densities themselves. The standard fraction of variance explained (FVE) criterion commonly used for functional data is adapted to the transformation setting, also allowing for an alternative quantification of variability for density data through the Wasserstein metric of optimal transport.
Author: A. Petersen, P. Z. Hadjipantelis and H.G. Mueller
Maintainer: Alexander Petersen <petersen@pstat.ucsb.edu>

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Package dynr updated to version 0.1.12-5 with previous version 0.1.11-8 dated 2017-08-21

Title: Dynamic Modeling in R
Description: Intensive longitudinal data have become increasingly prevalent in various scientific disciplines. Many such data sets are noisy, multivariate, and multi-subject in nature. The change functions may also be continuous, or continuous but interspersed with periods of discontinuities (i.e., showing regime switches). The package 'dynr' (Dynamic Modeling in R) is an R package that implements a set of computationally efficient algorithms for handling a broad class of linear and nonlinear discrete- and continuous-time models with regime-switching properties under the constraint of linear Gaussian measurement functions. The discrete-time models can generally take on the form of a state- space or difference equation model. The continuous-time models are generally expressed as a set of ordinary or stochastic differential equations. All estimation and computations are performed in C, but users are provided with the option to specify the model of interest via a set of simple and easy-to-learn model specification functions in R. Model fitting can be performed using single- subject time series data or multiple-subject longitudinal data.
Author: Lu Ou [aut], Michael D. Hunter [aut, cre], Sy-Miin Chow [aut]
Maintainer: Michael D. Hunter <mhunter.ou@gmail.com>

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Package rcartocolor updated to version 0.0.22 with previous version 0.0.21 dated 2017-11-06

Title: 'CARTOColors' Palettes
Description: Provides color schemes for maps and other graphics designed by 'CARTO' as described at <https://carto.com/carto-colors/>. It includes four types of palettes: aggregation, diverging, qualitative, and quantitative.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

Diff between rcartocolor versions 0.0.21 dated 2017-11-06 and 0.0.22 dated 2018-02-08

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Package hydrolinks updated to version 0.7.1 with previous version 0.5 dated 2017-11-06

Title: Hydrologic Network Linking Data and Tools
Description: Tools to link geographic data with hydrologic network, including lakes, streams and rivers. Includes automated download of U.S. National Hydrography Network and other hydrolayers.
Author: Tobi Hahn [aut], Luke Winslow [aut, cre], Taylor Leach [ctb], Kevin Rose [ths]
Maintainer: Luke Winslow <lawinslow@gmail.com>

Diff between hydrolinks versions 0.5 dated 2017-11-06 and 0.7.1 dated 2018-02-08

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Package CUB updated to version 1.1.2 with previous version 1.1 dated 2017-10-11

Title: A Class of Mixture Models for Ordinal Data
Description: For ordinal rating data, estimate and test models within the family of CUB models and their extensions (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions). Simulation routines, plotting facilities and fitting measures are also provided.
Author: Maria Iannario <maria.iannario@unina.it>, Domenico Piccolo <domenico.piccolo@unina.it>, Rosaria Simone <rosaria.simone@unina.it>
Maintainer: Rosaria Simone <rosaria.simone@unina.it>

Diff between CUB versions 1.1 dated 2017-10-11 and 1.1.2 dated 2018-02-08

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Package adjclust updated to version 0.5.6 with previous version 0.5.2 dated 2017-10-18

Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix
Description: Implements a constrained version of hierarchical agglomerative clustering, in which each observation is associated to a position, and only adjacent clusters can be merged. Typical application fields in bioinformatics include Genome-Wide Association Studies or Hi-C data analysis, where the similarity between items is a decreasing function of their genomic distance. Taking advantage of this feature, the implemented algorithm is time and memory efficient. This algorithm is described in Chapter 4 of Alia Dehman (2015) <https://hal.archives-ouvertes.fr/tel-01288568v1>.
Author: Christophe Ambroise [aut], Shubham Chaturvedi [aut], Alia Dehman [aut], Michel Koskas [aut], Pierre Neuvial [aut, cre], Guillem Rigaill [aut], Nathalie Villa-Vialaneix [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>

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More information about adjclust at CRAN
Permanent link

Package SWMPr updated to version 2.3.0 with previous version 2.2.0 dated 2016-11-07

Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <http://cdmo.baruch.sc.edu/>. These tools address common challenges associated with continuous time series data for environmental decision making.
Author: Marcus W. Beck [aut, cre], Kimberly Cressman [ctb]
Maintainer: Marcus W. Beck <marcusb@sccwrp.org>

Diff between SWMPr versions 2.2.0 dated 2016-11-07 and 2.3.0 dated 2018-02-08

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Permanent link

New package specklestar with initial version 0.0.1.7
Package: specklestar
Version: 0.0.1.7
Title: Reduction of Speckle Data from BTA 6-m Telescope
Description: A set of functions for obtaining positional parameters and magnitude difference between components of binary and multiple stellar systems from series of speckle images.
Author: Denis Rastegaev
Maintainer: Denis Rastegaev <drastega@gmail.com>
URL: https://drastega.github.io/docs/specklestar_vignette.html
BugReports: https://github.com/drastega/specklestar/issues
Depends: R (>= 3.0.0)
Imports: Rcpp
Suggests: imager, tidyverse, rgl, fftw, mrbsizeR, knitr, rmarkdown
License: GPL-2
NeedsCompilation: yes
SystemRequirements: fftw3 (>= 3.1.2)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Packaged: 2018-02-08 13:50:57 UTC; leda
Repository: CRAN
Date/Publication: 2018-02-08 18:14:49 UTC

More information about specklestar at CRAN
Permanent link

New package qcQpcr with initial version 1.5
Package: qcQpcr
Type: Package
Title: Histone ChIP-Seq qPCR Analyzer
Version: 1.5
Date: 2018-02-02
Author: Alireza Lorzadeh
Maintainer: Alireza Lorzadeh <alorzadeh@bcgsc.ca>
Description: Quality control of chromatin immunoprecipitation libraries (ChIP-seq) by quantitative polymerase chain reaction (qPCR). This function calculates Enrichment value with respect to reference for each histone modification (specific to 'Vii7' software <http://www.thermofisher.com/ca/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/viia-7-real-time-pcr-system/viia-7-software.html>). This function is applicable to full panel of histone modifications described by International Human Epigenomic Consortium (IHEC).
Imports: ggplot2
License: MIT + file LICENSE
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2018-02-08 18:09:49 UTC; epigenomics_lab_01
Repository: CRAN
Date/Publication: 2018-02-08 18:44:50 UTC

More information about qcQpcr at CRAN
Permanent link

Package micromap updated to version 1.9.3 with previous version 1.9.2 dated 2015-02-06

Title: Linked Micromap Plots
Description: This group of functions simplifies the creation of linked micromap plots.
Author: Quinn Payton [aut], Tony Olsen [aut], Marc Weber [ctb], Michael McManus [ctb], Tom Kincaid [ctb], Marcus W. Beck [cre, ctb]
Maintainer: Marcus W. Beck <marcusb@sccwrp.org>

Diff between micromap versions 1.9.2 dated 2015-02-06 and 1.9.3 dated 2018-02-08

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Permanent link

Package adepro updated to version 2.0.0 with previous version 0.1.0 dated 2017-07-12

Title: A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles
Description: Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Author: Nicole Mentenich, Jens Hooge, Bastian Becker, Christoph Tasto
Maintainer: Nicole Mentenich <nicole.mentenich@bayer.com>

Diff between adepro versions 0.1.0 dated 2017-07-12 and 2.0.0 dated 2018-02-08

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Package BayesGOF updated to version 2.1 with previous version 1.4 dated 2018-01-05

Title: Bayesian Modeling via Goodness of Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. (2018, Technical Report, <arXiv:1802.00474>).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>

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Package vqtl updated to version 2.0.0 with previous version 1.2.0 dated 2017-06-14

Title: Genome Scans to Accommodate and Target Genetic and Non-Genetic Effects on Trait Variance in Test Crosses
Description: In recognition that there are many factors (genetic loci, macro- genetic factors such as sex, and environmental factors) that influence the extent of environmental variation, the 'vqtl' package conducts genome scans that accommodate and target these factors. The main functions of this package, scanonevar() and scanonevar.perm() take as input a cross object from the popular 'qtl' package.
Author: Robert Corty [aut, cre]
Maintainer: Robert Corty <rcorty@gmail.com>

Diff between vqtl versions 1.2.0 dated 2017-06-14 and 2.0.0 dated 2018-02-08

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 vqtl-2.0.0/vqtl/man/scanonevar.boot.Rd                            |only
 vqtl-2.0.0/vqtl/man/scanonevar.perm.Rd                            |    4 
 vqtl-2.0.0/vqtl/tests/testthat/test-2-scanonevar.R                |  172 +++++
 vqtl-2.0.0/vqtl/tests/testthat/test-3-scanonevar.perm.R           |  221 +++----
 vqtl-2.0.0/vqtl/tests/testthat/test-4-plots.R                     |  246 ++++----
 vqtl-2.0.0/vqtl/tests/testthat/test-5-scanonevar.boot.R           |only
 35 files changed, 949 insertions(+), 733 deletions(-)

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Package ggmuller updated to version 0.4 with previous version 0.3 dated 2017-10-20

Title: Create Muller Plots of Evolutionary Dynamics
Description: Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits).
Author: Robert Noble [aut, cre] (<https://orcid.org/0000-0002-8057-4252>)
Maintainer: Robert Noble <robjohnnoble@gmail.com>

Diff between ggmuller versions 0.3 dated 2017-10-20 and 0.4 dated 2018-02-08

 DESCRIPTION             |    8 ++---
 MD5                     |   12 ++++----
 R/MullerPlot.R          |   71 +++++++++++++++++++++++++++++++++++++-----------
 README.md               |    6 ++--
 inst/doc/ggmuller.html  |   21 +++++++-------
 man/add_start_points.Rd |   21 +++++++++++---
 man/get_Muller_df.Rd    |   19 +++++++++++-
 7 files changed, 115 insertions(+), 43 deletions(-)

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Package EmiStatR updated to version 1.2.0.6 with previous version 1.2.0.4 dated 2018-01-30

Title: Emissions and Statistics in R for Wastewater and Pollutants in Combined Sewer Systems
Description: Provides a fast and parallelised calculator to estimate combined wastewater emissions. It supports the planning and design of urban drainage systems, without the requirement of extensive simulation tools. The 'EmiStatR' package implements modular R methods. This enables to add new functionalities through the R framework. Furthermore, 'EmiStatR' was implemented with an interactive user interface with sliders and input data exploration.
Author: J.A. Torres-Matallana [aut, cre] K. Klepiszewski [aut, cre] U. Leopold [ctb] G. Schutz [ctb] G.B.M. Heuvelink [ctb]
Maintainer: J.A. Torres-Matallana <arturo.torres@list.lu>

Diff between EmiStatR versions 1.2.0.4 dated 2018-01-30 and 1.2.0.6 dated 2018-02-08

 DESCRIPTION             |    8 ++++----
 MD5                     |   10 +++++-----
 R/Class-input.R         |    6 +++---
 R/EmiStatR.R            |   24 +++++++++++++++---------
 man/EmiStatR-package.Rd |    4 ++--
 man/input-class.Rd      |    6 +++---
 6 files changed, 32 insertions(+), 26 deletions(-)

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Package OutliersO3 updated to version 0.5.4 with previous version 0.5.3 dated 2018-02-06

Title: Draws Overview of Outliers (O3) Plots
Description: Potential outliers are identified for all combinations of a dataset's variables. The available methods are HDoutliers() from the package 'HDoutliers', FastPCS() from the package 'FastPCS', mvBACON() from 'robustX', adjOutlyingness() from 'robustbase', DectectDeviatingCells() from 'cellWise', covMcd() from 'robustbase'.
Author: Antony Unwin
Maintainer: Antony Unwin <unwin@math.uni-augsburg.de>

Diff between OutliersO3 versions 0.5.3 dated 2018-02-06 and 0.5.4 dated 2018-02-08

 DESCRIPTION                         |    8 ++++----
 MD5                                 |   26 +++++++++++++-------------
 NEWS                                |    5 +++++
 build/vignette.rds                  |binary
 inst/doc/O3-alphas-vignette.Rmd     |    2 +-
 inst/doc/O3-alphas-vignette.html    |   14 +++++++-------
 inst/doc/O3-newMethod-vignette.Rmd  |    2 +-
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 inst/doc/O3-pcps-vignette.Rmd       |    2 +-
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 vignettes/O3-alphas-vignette.Rmd    |    2 +-
 vignettes/O3-newMethod-vignette.Rmd |    2 +-
 vignettes/O3-pcps-vignette.Rmd      |    2 +-
 14 files changed, 43 insertions(+), 38 deletions(-)

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New package ITNr with initial version 0.1.0
Package: ITNr
Type: Package
Title: Analysis of the International Trade Network
Version: 0.1.0
Author: Matthew Smith
Maintainer: Matthew Smith <matt_smith.90@hotmail.co.uk>
Description: Functions to clean and process international trade data into an international trade network (ITN) are provided. It then provides a set a functions to undertake analysis and plots of the ITN (extract the backbone, centrality, blockmodels, clustering). Examining the key players in the ITN and regional trade patterns.
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
Imports: stats,circlize,GoodmanKruskal,graphics,RColorBrewer,reshape2,blockmodeling,igraph,utils,plyr,dplyr,statnet,animation,Matrix,cowplot,ggplot2,GGally,fastmatch,intergraph,sna,tnet,WDI,network,xergm,xergm.common,networkDynamic,ndtv
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-08 11:08:00 UTC; matt_
Repository: CRAN
Date/Publication: 2018-02-08 12:26:22 UTC

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New package amt with initial version 0.0.2.0
Package: amt
Type: Package
Title: Animal Movement Tools
Version: 0.0.2.0
Authors@R: c(person("Johannes","Signer", role = c("aut", "cre"), email = "jsigner@gwdg.de"))
Description: Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses (resource and step-selection functions), and simulation of space-use from fitted step-selection functions.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10), tidyverse, survival
Imports: broom, circular, dplyr (>= 0.7.0), fitdistrplus, FNN, geosphere, graphics, grDevices, lazyeval, leaflet, lubridate, maptools, methods, purrr, raster, Rcpp (>= 0.12.7), rgeos, rlang, sp, stats, tibble, tidyr, utils
Suggests: adehabitatLT, bcpa, ctmm, devtools, move, moveHMM, spacetime, testthat, trajectories, knitr, rmarkdown
LinkingTo: Rcpp
RoxygenNote: 6.0.1
RdMacros: Rdpack
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-02-08 12:01:39 UTC; jsigner
Author: Johannes Signer [aut, cre]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Repository: CRAN
Date/Publication: 2018-02-08 12:31:26 UTC

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New package SDLfilter with initial version 1.0.0
Package: SDLfilter
Type: Package
Title: Filtering Satellite-Derived Locations
Version: 1.0.0
Date: 2018-02-07
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <takahiro.shimada@my.jcu.edu.au>
Description: Functions to filter GPS and/or Argos locations. The provided filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as proposed in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>.
Depends: R (>= 2.10), raster, trip, data.table, geosphere
Imports: sp
License: GPL-2 | file LICENSE
URL: https://github.com/TakahiroShimada/SDLfilter
BugReports: https://github.com/TakahiroShimada/SDLfilter/issues
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-07 23:10:29 UTC; ubuntu
Repository: CRAN
Date/Publication: 2018-02-08 11:53:10 UTC

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New package codemetar with initial version 0.1.3
Package: codemetar
Type: Package
Title: Generate 'CodeMeta' Metadata for R Packages
Version: 0.1.3
Authors@R: person("Carl", "Boettiger", role=c("aut", "cre", "cph"), email="cboettig@gmail.com", comment=c(ORCID = "0000-0002-1642-628X"))
Description: The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
License: MIT + file LICENSE
URL: https://github.com/ropensci/codemetar
BugReports: https://github.com/ropensci/codemetar/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R (>= 3.0.0)
Imports: jsonlite (>= 1.3), jsonld, git2r, devtools, methods, stats, stringi, readr
Suggests: testthat, jsonvalidate, covr, knitr, rmarkdown, httr, magrittr, xml2, dplyr (>= 0.7.0), tibble, purrr, printr
VignetteBuilder: knitr
X-schema.org-keywords: metadata, codemeta, ropensci, citation, credit, linked-data
X-schema.org-isPartOf: https://ropensci.org
X-schema.org-relatedLink: https://codemeta.github.io/codemetar
NeedsCompilation: no
Packaged: 2018-02-07 21:38:44 UTC; cboettig
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-08 10:21:02 UTC

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New package oc with initial version 1.01
Package: oc
Version: 1.01
Date: 2018-02-05
Title: Optimal Classification Roll Call Analysis Software
Author: Keith Poole <ktpoole@uga.edu>, Jeffrey Lewis <jblewis@ucla.edu>, James Lo <lojames@usc.edu> and Royce Carroll <rcarroll@rice.edu>
Maintainer: James Lo <lojames@usc.edu>
Depends: R (>= 2.3.1), pscl (>= 0.59)
Description: Estimates optimal classification (Poole 2000) <doi:10.1093/oxfordjournals.pan.a029814> scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
License: GPL-2
Repository: CRAN
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-02-06 22:21:12 UTC; jameslo
Date/Publication: 2018-02-08 09:03:19 UTC

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New package geozoning with initial version 1.0.0
Package: geozoning
Title: Zoning Methods for Spatial Data
Version: 1.0.0
Authors@R: c( person("Brigitte", "Charnomordic", email = "brigitte.charnomordic@inra.fr", role = c("aut")), person("Hazaël", "Jones", email = "hazael.jones@supagro.fr", role = c("aut", "cre")), person("Patrice", "Loisel", email = "patrice.loisel@inra.fr", role = c("aut")), person("Isabelle", "Sanchez", email = "isabelle.sanchez@inra.fr", role = c("ctb")), person("Ngoc-Phi", "Tran", email = "Ngoc-Phi.Tran@gmail.fr", role = c("ctr")))
Author: Brigitte Charnomordic [aut], Hazaël Jones [aut, cre], Patrice Loisel [aut], Isabelle Sanchez [ctb], Ngoc-Phi Tran [ctr]
Maintainer: Hazaël Jones <hazael.jones@supagro.fr>
Description: A zoning method and a numerical criterion for zoning quality are available in this package. The zoning method is based on a numerical criterion that evaluates the zoning quality. This criterion quantifies simultaneously how zones are heterogeneous on the whole map and how neighbouring zones are similar. This approach allows comparison between maps either with different zones or different labels, which is of importance for zone delineation algorithms aiming at maximizing inter-zone variability. An optimisation procedure provides the user with the best zonings thanks to contour delineation for a given map.
Depends: R (>= 3.3.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: gstat, RandomFields, sp, maptools, deldir, fields, raster, graphics, stats, utils,grDevices, rgeos, ggplot2
Suggests: rmarkdown, knitr
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-07 08:11:18 UTC; sanchezi
Repository: CRAN
Date/Publication: 2018-02-08 09:58:39 UTC

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New package CoDiNA with initial version 1.0.0
Package: CoDiNA
Type: Package
Title: Co-Expression Differential Network Analysis
Version: 1.0.0
Author: Deisy Morselli Gysi, Tiago de Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Description: Categorize links from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks. More information about the methodology can be found at: Gysi et. al., 2018 <arXiv:1802.00828>.
License: GPL-2
LazyData: TRUE
Depends: R (>= 3.1)
Imports: data.table, igraph, magrittr, plyr, parallel, visNetwork, reshape2, geometry, plot3D
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-02-07 17:13:34 UTC; deisy
Repository: CRAN
Date/Publication: 2018-02-08 09:54:51 UTC

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New package adnuts with initial version 1.0.0
Package: adnuts
Title: No-U-Turn MCMC Sampling for 'ADMB' and 'TMB' Models
Version: 1.0.0
Authors@R: person("Cole", "Monnahan", email = "monnahc@uw.edu", role = c("aut", "cre"))
Description: Bayesian inference using the no-U-turn (NUTS) algorithm by Hoffman and Gelman (2014) <http://www.jmlr.org/papers/v15/hoffman14a.html>. Designed for 'AD Model Builder' ('ADMB') models, or when R functions for log-density and log-density gradient are available, such as 'Template Model Builder' ('TMB') models and other special cases. Functionality is similar to 'Stan', and the 'rstan' and 'shinystan' packages are used for diagnostics and inference.
Depends: R (>= 3.3.0)
URL: https://github.com/colemonnahan/adnuts
BugReports: https://github.com/colemonnahan/adnuts/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
ByteCompile: true
Suggests: snowfall (>= 1.84.6.1), shinystan (>= 2.3.0), R2admb (>= 0.7.15), matrixcalc (>= 1.0.3), TMB (>= 1.7.11), stats, knitr, rmarkdown
Imports: ellipse, rstan
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-07 16:39:25 UTC; Cole
Author: Cole Monnahan [aut, cre]
Maintainer: Cole Monnahan <monnahc@uw.edu>
Repository: CRAN
Date/Publication: 2018-02-08 09:49:24 UTC

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Package model4you updated to version 0.9-1 with previous version 0.9-0 dated 2018-01-16

Title: Stratified and Personalised Models Based on Model-Based Trees and Forests
Description: Model-based trees for subgroup analyses in clinical trials and model-based forests for the estimation and prediction of personalised treatment effects (personalised models). Currently partitioning of linear models, lm(), generalised linear models, glm(), and Weibull models, survreg(), is supported. Advanced plotting functionality is supported for the trees and a test for parameter heterogeneity is provided for the personalised models. For details on model-based trees for subgroup analyses see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for details on model-based forests for estimation of individual treatment effects see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre], Achim Zeileis [aut], Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>

Diff between model4you versions 0.9-0 dated 2018-01-16 and 0.9-1 dated 2018-02-08

 model4you-0.9-0/model4you/man/objfun.pmodel.identity.Rd |only
 model4you-0.9-0/model4you/man/test_heterogeneity.Rd     |only
 model4you-0.9-1/model4you/DESCRIPTION                   |    8 +-
 model4you-0.9-1/model4you/MD5                           |   38 ++++++------
 model4you-0.9-1/model4you/NAMESPACE                     |    6 +-
 model4you-0.9-1/model4you/R/objfun.R                    |    2 
 model4you-0.9-1/model4you/R/plot-pmtree.R               |   16 +++--
 model4you-0.9-1/model4you/R/pmforest.R                  |    2 
 model4you-0.9-1/model4you/R/pmodel-methods.R            |   32 +++++-----
 model4you-0.9-1/model4you/R/pmodel-test.R               |   47 +++++++++-------
 model4you-0.9-1/model4you/R/pmodel.R                    |    6 +-
 model4you-0.9-1/model4you/R/pmtree-methods.R            |   42 ++++++++++----
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 23 files changed, 148 insertions(+), 85 deletions(-)

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Package dendroTools updated to version 0.0.6 with previous version 0.0.5 dated 2018-01-04

Title: Linear and Nonlinear Methods for Analyzing Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the Tree-ring research community. There are two core functions. The first one is daily_response(), which finds the optimal sequence of days that are related to one or more tree-ring proxy records. The second one is compare_methods(), which effectively compares several linear and nonlinear regression algorithms.
Author: Jernej Jevsenak [aut, cre], Tom Levanic [ctb]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>

Diff between dendroTools versions 0.0.5 dated 2018-01-04 and 0.0.6 dated 2018-02-08

 DESCRIPTION                           |   13 
 MD5                                   |   37 -
 NAMESPACE                             |    5 
 NEWS.md                               |   22 
 R/calculate_metrics.R                 |    6 
 R/compare_methods.R                   |  855 +++++++++++++++++-----------------
 R/daily_response.R                    |   25 
 R/data_TRW.R                          |    2 
 R/plot_specific.R                     |    2 
 R/smooth_matrix.R                     |    4 
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 man/compare_methods.Rd                |  101 ++--
 man/daily_response.Rd                 |   22 
 man/data_TRW.Rd                       |    2 
 man/plot_specific.Rd                  |   25 
 man/smooth_matrix.Rd                  |    4 
 vignettes/Examples_daily_response.Rmd |    6 
 20 files changed, 592 insertions(+), 599 deletions(-)

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Package cmsaf updated to version 1.9.0 with previous version 1.8.1 dated 2017-07-11

Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable observing of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of seven National Meteorological and Hydrological Services. The 'cmsaf' R-package provides a collection of R-operators for the analysis and manipulation of CM SAF NetCDF formatted data. The 'cmsaf' R-package is tested for CM SAF NetCDF data, which are structured in three-dimensional arrays (longitude, latitude, time) on a rectangular grid. Layered CM SAF data have to be converted with the provided levbox_mergetime() function. The 'cmsaf' R-package operators have only minor checks for deviations from the recommended data structure, and give only few specific error messages. Scripts for an easy application of the 'cmsaf' package operators and the preparation and visualization of CM SAF NetCDF data are provided at the CM SAF webpage (<http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html>).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

Diff between cmsaf versions 1.8.1 dated 2017-07-11 and 1.9.0 dated 2018-02-08

 DESCRIPTION          |   31 ++++++-------
 MD5                  |   44 ++++++++++---------
 NAMESPACE            |    4 +
 R/box_mergetime.R    |   25 ++++++++---
 R/checkfile.R        |   34 +++++++++------
 R/cmsaf.cat.R        |only
 R/fldmax.R           |   43 +++++++++++--------
 R/fldmean.R          |   39 ++++++++++-------
 R/fldmin.R           |   43 +++++++++++--------
 R/levbox_mergetime.R |   35 +++++++++++++--
 R/monsum.R           |   18 ++++----
 R/multimonmean.R     |   13 +++--
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 R/remapbil.R         |    6 +-
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 R/wfldmean.R         |    2 
 R/yearsum.R          |    4 +
 man/box_mergetime.Rd |    1 
 man/cmsaf-package.Rd |    9 +---
 man/cmsaf.cat.Rd     |only
 man/timpctl.Rd       |only
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 25 files changed, 355 insertions(+), 203 deletions(-)

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