Tue, 31 Jul 2018

Package huxtable updated to version 4.1.0 with previous version 4.0.1 dated 2018-07-03

Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Like 'xtable', creates styled tables. Export to HTML, LaTeX, 'Word', 'Excel', 'PowerPoint' and other formats. Simple, modern interface to manipulate borders, size, position, captions, colours, text styles and number formatting. Table cells can span multiple rows and/or columns. Includes a 'huxreg' function for creation of regression tables, and 'quick_*' one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

Diff between huxtable versions 4.0.1 dated 2018-07-03 and 4.1.0 dated 2018-07-31

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Package funModeling updated to version 1.6.8 with previous version 1.6.7 dated 2018-01-21

Title: Exploratory Data Analysis and Data Preparation Tool-Box Book
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<http://livebook.datascienceheroes.com/>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas [aut, cre]
Maintainer: Pablo Casas <pcasas.biz@gmail.com>

Diff between funModeling versions 1.6.7 dated 2018-01-21 and 1.6.8 dated 2018-07-31

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Package statip updated to version 0.2.0 with previous version 0.1.5 dated 2017-11-05

Title: Statistical Functions for Probability Distributions and Regression
Description: A collection of miscellaneous statistical functions for probability distributions: dbern(), pbern(), qbern(), rbern() for the Bernoulli distribution, and distr2name(), name2distr() for distribution names; probability density estimation: densityfun(); most frequent value estimation: mfv(), mfv1(); calculation of the Hellinger distance: hellinger(); use of classical kernels: kernelfun(), kernel_properties(); univariate piecewise-constant regression: picor().
Author: Paul Poncet [aut, cre], The R Core Team [aut, cph] (C function 'BinDist' copied from package 'stats'), The R Foundation [cph] (C function 'BinDist' copied from package 'stats'), Adrian Baddeley [ctb] (C function 'BinDist' copied from package 'stats')
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between statip versions 0.1.5 dated 2017-11-05 and 0.2.0 dated 2018-07-31

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Package geomerge updated to version 0.3.1 with previous version 0.3.0 dated 2017-08-28

Title: Geospatial Data Integration
Description: Geospatial data integration framework that merges raster, spatial polygon, and (dynamic) spatial points data into a spatial (panel) data frame at any geographical resolution.
Author: Karsten Donnay and Andrew M. Linke
Maintainer: Karsten Donnay <kdonnay@gmx.net>

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Package flifo updated to version 0.1.5 with previous version 0.1.4 dated 2017-01-14

Title: Don't Get Stuck with Stacks in R
Description: Functions to create and manipulate FIFO (First In First Out), LIFO (Last In First Out), and NINO (Not In or Never Out) stacks in R.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between flifo versions 0.1.4 dated 2017-01-14 and 0.1.5 dated 2018-07-31

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Package bazar updated to version 1.0.9 with previous version 1.0.6 dated 2017-11-14

Title: Miscellaneous Basic Functions
Description: A collection of miscellaneous functions for copying objects to the clipboard ('Copy'); manipulating strings ('concat', 'mgsub', 'trim', 'verlan'); loading or showing packages ('library_with_dep', 'require_with_dep', 'sessionPackages'); creating or testing for named lists ('nlist', 'as.nlist', 'is.nlist'), formulas ('is.formula'), empty objects ('as.empty', 'is.empty'), whole numbers ('as.wholenumber', 'is.wholenumber'); testing for equality ('almost.equal', 'almost.zero') and computing uniqueness ('almost.unique'); getting modified versions of usual functions ('rle2', 'sumNA'); making a pause or a stop ('pause', 'stopif'); converting into a function ('as.fun'); providing a C like ternary operator ('condition %?% true %:% false'); finding packages and functions ('get_all_pkgs', 'get_all_funs'); and others ('erase', '%nin%', 'unwhich', 'top', 'bot', 'normalize').
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

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Package RQEntangle updated to version 0.1.2 with previous version 0.1.1 dated 2018-06-21

Title: Quantum Entanglement of Bipartite System
Description: It computes the Schmidt decomposition of bipartite quantum systems, discrete or continuous, and their respective entanglement metrics. See Artur Ekert, Peter L. Knight (1995) <doi:10.1119/1.17904> for more details.
Author: Kwan-Yuet Ho [aut, cre]
Maintainer: Kwan-Yuet Ho <stephenhky@yahoo.com.hk>

Diff between RQEntangle versions 0.1.1 dated 2018-06-21 and 0.1.2 dated 2018-07-31

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New package anyflights with initial version 0.1.0
Package: anyflights
Title: Download Air Travel Data for Specified Years and Airports
Version: 0.1.0
Authors@R: c( person("Simon P.", "Couch", , "simonpatrickcouch@gmail.com", c("aut", "cre")), person("Jay", "Lee", , "jaylee@reed.edu", "aut"), person("Hadley", "Wickham", , "hadley@rstudio.com", "aut"), person("RStudio", role = "cph") )
Description: Supplies a set of functions to query air travel data for user- specified years and airports. Datasets include on-time flights, airlines, airports, and weather.
License: CC0
LazyData: true
Depends: R (>= 2.10)
Imports: httr, dplyr, readr, RCurl, utils, tibble, lubridate
URL: http://github.com/simonpcouch/anyflights
BugReports: https://github.com/simonpcouch/anyflights/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-07-31 15:23:40 UTC; simonpcouch
Author: Simon P. Couch [aut, cre], Jay Lee [aut], Hadley Wickham [aut], RStudio [cph]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-31 16:10:03 UTC

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New package phylotaR with initial version 1.0.0
Package: phylotaR
Type: Package
Title: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
Version: 1.0.0
Authors@R: c(person("Hannes", "Hettling", role = "aut"), person("Rutger", "Vos", role = "aut"), person("Alexander", "Zizka", role = "aut"), person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com"), person("Alexandre", "Antonelli", role = c("aut")))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
License: MIT + file LICENSE
URL: https://github.com/ropensci/phylotaR#readme
BugReports: https://github.com/ropensci/phylotaR/issues
SystemRequirements: BLAST+ (>=2.0)
Depends: R (>= 3.3.0), methods,
Imports: igraph, rentrez, XML, ggplot2, sys, treeman, treemapify, R.utils
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2018-07-31 14:02:27 UTC; dom
Author: Hannes Hettling [aut], Rutger Vos [aut], Alexander Zizka [aut], Dom Bennett [aut, cre], Alexandre Antonelli [aut]
Repository: CRAN
Date/Publication: 2018-07-31 15:50:03 UTC

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Package Kernelheaping updated to version 2.2.0 with previous version 2.1.8 dated 2017-10-10

Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymised data the user often encounters heaped data, i.e. data which are rounded (to a possibly different degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well: Gross, M. and Rendtel, U. (2016) (<doi:10.1093/jssam/smw011>). Additionally, bivariate non-parametric density estimation for rounded data, Gross, M. et al. (2016) (<doi:10.1111/rssa.12179>), as well as data aggregated on areas is supported.
Author: Marcus Gross [aut, cre], Kerstin Erfurth [ctb]
Maintainer: Marcus Gross <marcus.gross@inwt-statistics.de>

Diff between Kernelheaping versions 2.1.8 dated 2017-10-10 and 2.2.0 dated 2018-07-31

 DESCRIPTION           |   10 +++++-----
 MD5                   |    8 ++++----
 R/functions.R         |   26 +++++++++++++++-----------
 man/dshapebivr.Rd     |    6 +++---
 man/dshapebivrProp.Rd |    8 ++++----
 5 files changed, 31 insertions(+), 27 deletions(-)

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New package jmdl with initial version 0.1.0
Package: jmdl
Type: Package
Title: Joint Mean-Correlation Regression Approach for Discrete Longitudinal Data
Version: 0.1.0
Author: Jane Lee
Maintainer: Jane Lee <mote@mail.ustc.edu.cn>
Description: Fit joint mean-correlation models for discrete longitudinal data (Tang CY,Zhang W, Leng C, 2017 <doi:10.5705/ss.202016.0435>).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
Imports: Formula, methods, minqa, boot, mnormt, MASS, mvtnorm, abind
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-07-31 13:37:36 UTC; ThinkPad
Repository: CRAN
Date/Publication: 2018-07-31 15:50:17 UTC

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New package alpaca with initial version 0.2
Package: alpaca
Type: Package
Title: Fit GLM's with High-Dimensional k-Way Fixed Effects
Version: 0.2
Authors@R: c(person("Amrei", "Stammann", email = "amrei.stammann@hhu.de", role = c("aut", "cre")), person("Daniel", "Czarnowske", email = "daniel.czarnowske@hhu.de", role = c("aut")))
Description: Provides a routine to concentrate out factors with many levels during the optimization of the log-likelihood function of the corresponding generalized linear model (glm). The package is based on the algorithm proposed by Stammann (2018) <arXiv:1707.01815> and is restricted to glm's that are based on maximum likelihood estimation and non-linear. It also offers an efficient algorithm to recover estimates of the fixed effects in a post-estimation routine. The package also includes robust and multi-way clustered standard errors.
License: GPL-3
Depends: R (>= 3.1.0)
Imports: data.table, Formula, MASS, Rcpp, stats, utils
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/amrei-stammann/alpaca
BugReports: https://github.com/amrei-stammann/alpaca/issues
RoxygenNote: 6.1.0
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-31 15:12:05 UTC; daniel
Author: Amrei Stammann [aut, cre], Daniel Czarnowske [aut]
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Repository: CRAN
Date/Publication: 2018-07-31 16:00:02 UTC

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Package gcKrig updated to version 1.1.2 with previous version 1.1.1 dated 2017-10-08

Title: Analysis of Geostatistical Count Data using Gaussian Copulas
Description: Provides a variety of functions to analyze and model geostatistical count data with Gaussian copulas, including 1) data simulation and visualization; 2) correlation structure assessment (here also known as the Normal To Anything); 3) calculate multivariate normal rectangle probabilities; 4) likelihood inference and parallel prediction at predictive locations.
Author: Zifei Han
Maintainer: Zifei Han <hanzifei1@gmail.com>

Diff between gcKrig versions 1.1.1 dated 2017-10-08 and 1.1.2 dated 2018-07-31

 DESCRIPTION    |    6 -
 MD5            |    8 -
 R/TwoMethods.R |  276 ++++++++++++++++++++++++++++-----------------------------
 R/gcClass.R    |    2 
 inst/NEWS.txt  |   11 ++
 5 files changed, 157 insertions(+), 146 deletions(-)

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New package ARIbrain with initial version 0.1
Package: ARIbrain
Version: 0.1
Date: 2018-07-27
Title: All-Resolution Inference
Author: Livio Finos, Jelle Goeman, Wouter Weeda, Jonathan Rosenblatt, Aldo Solari
Maintainer: Livio Finos <livio.finos@unipd.it>
Description: It performs All-Resolutions Inference (ARI) on functional Magnetic Resonance Image (fMRI) data. As a main feature, it estimates lower bounds for the proportion of active voxels in a set of clusters as, for example, given by a cluster-wise analysis. The method is described in Rosenblatt, Finos, Weeda, Solari, Goeman (2018) <doi:10.1016/j.neuroimage.2018.07.060>.
License: GPL (>= 2)
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
Imports: hommel, RNifti, plyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 13:22:45 UTC; livio
Repository: CRAN
Date/Publication: 2018-07-31 14:50:03 UTC

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Package MEPDF updated to version 2.0 with previous version 1.0 dated 2017-10-25

Title: Creation of Empirical Density Functions Based on Multivariate Data
Description: Based on the input data an n-dimensional cube with sub cells of user specified side length is created. The number of sample points which fall in each sub cube is counted, and with the cell volume and overall sample size an empirical probability can be computed. A number of cubes of higher resolution can be superimposed. The basic method stems from J.L. Bentley in "Multidimensional Divide and Conquer". J. L. Bentley (1980) <doi:10.1145/358841.358850>. Furthermore a simple kernel density estimation method is made available, as well as an expansion of Bentleys method, which offers a kernel approach for the grid method.
Author: Martin Wiegand, Saralees Nadarajah
Maintainer: Martin Wiegand <Martin.Wiegand@manchester.ac.uk>

Diff between MEPDF versions 1.0 dated 2017-10-25 and 2.0 dated 2018-07-31

 DESCRIPTION         |   17 +++--
 MD5                 |   12 ++-
 NAMESPACE           |    9 +-
 R/EPDF.R            |  171 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 man/ekde.Rd         |only
 man/epakernel.Rd    |only
 man/epdf.Rd         |    2 
 man/normkernel.Rd   |only
 man/pseudokernel.Rd |only
 9 files changed, 191 insertions(+), 20 deletions(-)

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New package uniformly with initial version 0.1.0
Package: uniformly
Type: Package
Title: Uniform Sampling
Version: 0.1.0
Date: 2018-07-31
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Description: Uniform sampling on various geometric shapes, such as spheres, ellipsoids, simplices.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/stla/uniformly
BugReports: https://github.com/stla/uniformly/issues
RoxygenNote: 6.0.1
Imports: stats, pgnorm
Suggests: knitr, rmarkdown, geometry, rgl, misc3d, scatterplot3d
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 06:53:14 UTC; SDL96354
Repository: CRAN
Date/Publication: 2018-07-31 12:10:03 UTC

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New package tm1r with initial version 1.0.0
Package: tm1r
Type: Package
Title: The Integration Between 'IBM COGNOS TM1' and R
Version: 1.0.0
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: jsonlite, httr
NeedsCompilation: no
Packaged: 2018-07-31 10:19:17 UTC; MAnd58
Repository: CRAN
Date/Publication: 2018-07-31 12:30:03 UTC

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Package maptools updated to version 0.9-3 with previous version 0.9-2 dated 2017-03-25

Title: Tools for Reading and Handling Spatial Objects
Description: Set of tools for manipulating and reading geographic data, in particular 'ESRI Shapefiles'; C code used from 'shapelib'. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', 'RArcInfo', 'Stata tmap', 'WinBUGS', 'Mondrian', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Nicholas Lewin-Koh [aut], Edzer Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb], Nick Bearman [ctb], Hans-Jörg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan [ctb], German Carrillo [ctb], Stéphane Dray [ctb], David Forrest [ctb], Michael Friendly [ctb], Patrick Giraudoux [ctb], Duncan Golicher [ctb], Virgilio Gómez Rubio [ctb], Patrick Hausmann [ctb], Karl Ove Hufthammer [ctb], Thomas Jagger [ctb], Kent Johnson [ctb], Sebastian Luque [ctb], Don MacQueen [ctb], Andrew Niccolai [ctb], Edzer Pebesma [ctb], Oscar Perpiñán Lamigueiro [ctb], Tom Short [ctb], Greg Snow [ctb], Ben Stabler [ctb], Murray Stokely [ctb], Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between maptools versions 0.9-2 dated 2017-03-25 and 0.9-3 dated 2018-07-31

 ChangeLog                     |  862 +-----------------------------------------
 DESCRIPTION                   |   14 
 MD5                           |   34 -
 R/AAA.R                       |   36 +
 R/Spatial-methods.R           |    4 
 R/SpatialLines-methods.R      |    4 
 R/SpatialPoints-methods.R     |    4 
 R/SpatialPolys-methods.R      |    4 
 R/spatstat1.R                 |   30 -
 build/vignette.rds            |binary
 inst/ChangeLog                |  862 +-----------------------------------------
 inst/doc/combine_maptools.pdf |binary
 man/kmlLines.Rd               |    4 
 man/kmlPolygons.Rd            |   10 
 man/readShapeLines.Rd         |    5 
 man/readShapePoints.Rd        |    5 
 man/readShapePoly.Rd          |    5 
 man/readShapeSpatial.Rd       |    5 
 18 files changed, 175 insertions(+), 1713 deletions(-)

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New package EMSHS with initial version 1.0.0
Package: EMSHS
Type: Package
Title: EM Algorithm for Bayesian Shrinkage Approach with Structural Information Incorporated
Version: 1.0.0
Author: Changgee Chang and Praveen Suthaharan
Maintainer: Praveen Suthaharan <psuthah@emory.edu>
Description: Fits a Bayesian shrinkage regression model that can incorporate structural information. Changgee Chang, Suprateek Kundu, Qi Long (2018) <doi:10.1111/biom.12882>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: Rdpack
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2018-07-31 10:44:34 UTC; prave
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2018-07-31 12:40:02 UTC

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New package cxhull with initial version 0.1.0
Package: cxhull
Type: Package
Title: Convex Hull
Version: 0.1.0
Date: 2018-07-31
Authors@R: c( person("C. B.", "Barber", role="cph", comment="author of the Qhull library"), person("The Geometry Center", role="cph"), person("Stéphane", "Laurent", role=c("cph","aut","cre"), email="laurent_step@yahoo.fr"))
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Description: Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/stla/cxhull
BugReports: https://github.com/stla/cxhull/issues
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, rgl
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-31 07:02:21 UTC; SDL96354
Author: C. B. Barber [cph] (author of the Qhull library), The Geometry Center [cph], Stéphane Laurent [cph, aut, cre]
Repository: CRAN
Date/Publication: 2018-07-31 12:20:02 UTC

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New package BDP2 with initial version 0.1.3
Package: BDP2
Type: Package
Title: Bayesian Adaptive Designs for Phase II Trials with Binary Endpoint
Version: 0.1.3
Date: 2018-07-31
Author: Annette Kopp-Schneider, Manuel Wiesenfarth, Ulrich Abel
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>
Description: Tools and workflow to choose design parameters in Bayesian adaptive single-arm phase II trial designs with binary endpoint (response, success) with possible stopping for efficacy and futility at interim analyses. Also contains routines to determine and visualize operating characteristics. See Kopp-Schneider et al. (2018) <doi:10.1002/bimj.201700209>.
License: GPL-2
Depends: rmarkdown, shiny, shinyBS
LazyData: TRUE
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 09:11:34 UTC; wiesenfa
Repository: CRAN
Date/Publication: 2018-07-31 12:30:06 UTC

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Package RobAStRDA updated to version 1.1.0 with previous version 1.0.2 dated 2016-04-25

Title: Interpolation Grids for Packages of the 'RobASt' - Family of Packages
Description: Includes 'sysdata.rda' file for packages of the 'RobASt' - family of packages; is currently used by package 'RobExtremes' only.
Author: Matthias Kohl [aut, cph], Bernhard Spangl [ctb] (contributed smoothed grid values of the Lagrange multipliers), Sascha Desmettre [ctb] (contributed smoothed grid values of the Lagrange multipliers), Eugen Massini [ctb] (contributed an interactive smoothing routine for smoothing the Lagrange multipliers and smoothed grid values of the Lagrange multipliers), Mykhailo Pupashenko [ctb] (helped with manual smoothing of the interpolators), Daria Pupashenko [ctb] (helped with manual smoothing of the interpolators), Gerald Kroisandt [ctb] (helped with manual smoothing of the interpolators), Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>

Diff between RobAStRDA versions 1.0.2 dated 2016-04-25 and 1.1.0 dated 2018-07-31

 DESCRIPTION                                              |   45 ++---
 MD5                                                      |   15 +
 NAMESPACE                                                |    8 -
 R/sysdata.rda                                            |binary
 inst/AddMaterial/interpolation/WriteUp-Interpolators.txt |   82 ++++++----
 inst/AddMaterial/interpolation/interpolationscripts.R    |  113 ++++++++++++++-
 inst/CITATION                                            |only
 inst/NEWS                                                |   10 +
 man/0RobRDA-package.Rd                                   |    8 -
 9 files changed, 209 insertions(+), 72 deletions(-)

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New package adaptMT with initial version 1.0.0
Package: adaptMT
Type: Package
Title: Adaptive P-Value Thresholding for Multiple Hypothesis Testing with Side Information
Version: 1.0.0
Authors@R: person("Lihua", "Lei", email = "lihua.lei@berkeley.edu", role = c("aut", "cre"))
Maintainer: Lihua Lei <lihua.lei@berkeley.edu>
Description: Implementation of adaptive p-value thresholding (AdaPT), including both a framework that allows the user to specify any algorithm to learn local false discovery rate and a pool of convenient functions that implement specific algorithms. See Lei, Lihua and Fithian, William (2016) <arXiv:1609.06035>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://arxiv.org/abs/1609.06035, https://github.com/lihualei71/adaptMT
BugReports: https://github.com/lihualei71/adaptMT/issues
Suggests: glmnet, HDtweedie, mgcv, splines, testthat, knitr, rmarkdown, dplyr
RoxygenNote: 6.0.1
Imports: methods
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 06:40:07 UTC; Leo
Author: Lihua Lei [aut, cre]
Repository: CRAN
Date/Publication: 2018-07-31 12:00:03 UTC

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New package SingleCaseES with initial version 0.4.0
Package: SingleCaseES
Type: Package
Title: A Calculator for Single-Case Effect Sizes
Version: 0.4.0
Date: 2018-07-28
Authors@R: c( person(c("James","E."), "Pustejovsky", email = "jepusto@gmail.com", role = c("aut", "cre")), person(c("Daniel","M."), "Swan", email = "dswan@utexas.edu", role = "aut") )
Description: Provides R functions for calculating basic effect size indices for single-case designs, including several non-overlap measures and parametric effect size measures, and for estimating the gradual effects model developed by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>. Standard errors and confidence intervals (based on the assumption that the outcome measurements are mutually independent) are provided for the subset of effect sizes indices with known sampling distributions.
URL: https://github.com/jepusto/SingleCaseES
BugReports: https://github.com/jepusto/SingleCaseES/issues
License: GPL-3
Imports: stats, purrr, magrittr, dplyr, tidyr, rlang, tidyselect
Suggests: spelling, shiny, ggplot2, testthat, markdown, knitr, rmarkdown, prettydoc, kableExtra
LazyData: TRUE
RoxygenNote: 6.0.1
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 21:08:57 UTC; jep2963
Author: James E. Pustejovsky [aut, cre], Daniel M. Swan [aut]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-31 10:20:06 UTC

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New package robmixglm with initial version 1.0-2
Package: robmixglm
Type: Package
Title: Robust Generalized Linear Models (GLM) using Mixtures
Version: 1.0-2
Date: 2018-07-31
Authors@R: c(person("Ken","Beath",email="ken.beath@mq.edu.au", role=c("aut","cre")))
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Contact: Ken Beath <ken.beath@mq.edu.au>
Author: Ken Beath [aut, cre]
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Depends: R(>= 3.2.0)
Suggests: R.rsp, robustbase, lattice, forward
VignetteBuilder: R.rsp
Imports: fastGHQuad, stats, bbmle, MASS, VGAM, actuar, Rcpp (>= 0.12.15), methods, boot, numDeriv
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
License: GPL (>= 2)
LinkingTo: Rcpp
Packaged: 2018-07-31 02:18:23 UTC; kjbeath1
Repository: CRAN
Date/Publication: 2018-07-31 10:40:03 UTC

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New package makeParallel with initial version 0.1.1
Package: makeParallel
Version: 0.1.1
Date: 2018-07-18
Title: Transform Serial R Code into Parallel R Code
Authors@R: person("Clark", "Fitzgerald", role = c("aut", "cre"), email = "clarkfitzg@gmail.com", comment = c(ORCID = "0000-0003-3446-6389"))
Maintainer: Clark Fitzgerald <clarkfitzg@gmail.com>
Depends: R (>= 3.1.0)
Imports: methods, utils, graphics, parallel, codetools, CodeDepends, whisker
Suggests: igraph, roxygen2, knitr, rmarkdown, testthat
Description: Writing parallel R code can be difficult, particularly for code that is not "embarrassingly parallel". This experimental package automates the transformation of serial R code into more efficient parallel versions. It identifies task parallelism by statically analyzing entire scripts to detect dependencies between statements. It implements an extensible system for scheduling and generating new code. It includes a reference implementation of the 'List Scheduling' approach to the general task scheduling problem of scheduling statements on multiple processors.
License: MIT + file LICENSE
URL: https://github.com/clarkfitzg/makeParallel
BugReports: https://github.com/clarkfitzg/makeParallel
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 19:23:01 UTC; clark
Author: Clark Fitzgerald [aut, cre] (<https://orcid.org/0000-0003-3446-6389>)
Repository: CRAN
Date/Publication: 2018-07-31 10:30:03 UTC

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New package LVGP with initial version 2.1.3
Package: LVGP
Type: Package
Title: Latent Variable Gaussian Process Modeling with Qualitative and Quantitative Input Variables
Version: 2.1.3
Author: Siyu Tao, Yichi Zhang
Maintainer: Siyu Tao <siyutao2020@u.northwestern.edu>
Description: Fit response surfaces for datasets with latent-variable Gaussian process modeling, predict responses for new inputs, and plot latent variables locations in the latent space (1D or 2D). The input variables of the datasets can be quantitative, qualitative/categorical or mixed. The output variable of the datasets is a scalar (quantitative). The method is published in "A Latent Variable Approach to Gaussian Process Modeling with Qualitative and Quantitative Factors" by Yichi Zhang, Siyu Tao, Wei Chen, and Daniel W. Apley (2018) <arXiv:1806.07504>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: lhs(>= 0.14), randtoolbox(>= 1.17), lattice(>= 0.20-34)
Depends: R (>= 3.5.0), stats (>= 3.2.5), parallel (>= 3.2.5)
Repository: CRAN
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-07-30 22:42:42 UTC; SiyuTao
Date/Publication: 2018-07-31 10:20:10 UTC

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New package geodetector with initial version 1.0-1
Package: geodetector
Title: Stratified Heterogeneity Measure, Dominant Driving Force Detection, Interaction Relationship Investigation
Version: 1.0-1
Authors@R: c(person("Chengdong", "Xu", email = "xucd@Lreis.ac.cn", role = c("aut", "cre")),person("Jinfeng", "Wang", email = "wangjf@Lreis.ac.cn", role = c("aut")),person("Yue", "Hou" , role = "ctb"),person("Qian", "Yin", role = "ctb"))
Description: Spatial stratified heterogeneity (SSH), referring to the within strata are more similar than the between strata, a model with global parameters would be confounded if input data is SSH. Note that the "spatial" here can be either geospatial or the space in mathematical meaning. Geographical detector is a novel tool to investigate SSH: (1) measure and find SSH of a variable Y; (2) test the power of determinant X of a dependent variable Y according to the consistency between their spatial distributions; and (3) investigate the interaction between two explanatory variables X1 and X2 to a dependent variable Y (Wang et al 2014 <doi:10.1080/13658810802443457>, Wang, Zhang, and Fu 2016 <doi:10.1016/j.ecolind.2016.02.052>).
Depends: R (>= 2.10)
Imports: sp (>= 1.2-7),rgeos (>= 0.3-26),rgdal (>= 1.2-16),maptools
License: GPL (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Author: Chengdong Xu [aut, cre], Jinfeng Wang [aut], Yue Hou [ctb], Qian Yin [ctb]
Maintainer: Chengdong Xu <xucd@Lreis.ac.cn>
Repository: CRAN
Packaged: 2018-07-31 01:56:47 UTC; lenovo
Date/Publication: 2018-07-31 10:40:06 UTC

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New package circumplex with initial version 0.1.1
Type: Package
Package: circumplex
Title: Analysis and Visualization of Circular Data
Version: 0.1.1
Authors@R: c( person("Jeffrey", "Girard", email = "me@jmgirard.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7359-3746")), person("Johannes", "Zimmermann", role = "aut", comment = c(ORCID = "0000-0001-6975-2356")), person("Aidan", "Wright", role = "aut", comment = c(ORCID = "0000-0002-2369-0601")) )
Description: Tools for analyzing and visualizing circular data, including a generalization of the bootstrapped structural summary method from Zimmermann & Wright (2017) <doi:10.1177/1073191115621795> and functions for creating publication-ready tables and figures from the results. Future versions will include tools for circular fit and reliability analyses, as well as greatly enhanced visualization methods.
License: GPL-3
URL: https://github.com/jmgirard/circumplex
BugReports: https://github.com/jmgirard/circumplex/issues
Depends: R (>= 3.5.0)
Imports: assertthat (>= 0.2.0), boot (>= 1.3.20), dplyr (>= 0.7.6), ggforce (>= 0.1.3), ggplot2 (>= 3.0.0), htmlTable (>= 1.12), magrittr (>= 1.5), purrr (>= 0.2.5), Rcpp (>= 0.12.18), rlang (>= 0.2.1), stats, tibble (>= 1.4.2), tidyr (>= 0.8.1)
LinkingTo: Rcpp (>= 0.12.18), RcppArmadillo (>= 0.8.600.0.0)
RoxygenNote: 6.1.0
Suggests: covr (>= 3.1.0), forcats (>= 0.3.0), kableExtra (>= 0.9.0), knitr (>= 1.20), psych (>= 1.8.4), rmarkdown (>= 1.10), testthat (>= 2.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-30 19:06:29 UTC; Eleventh
Author: Jeffrey Girard [aut, cre] (<https://orcid.org/0000-0002-7359-3746>), Johannes Zimmermann [aut] (<https://orcid.org/0000-0001-6975-2356>), Aidan Wright [aut] (<https://orcid.org/0000-0002-2369-0601>)
Maintainer: Jeffrey Girard <me@jmgirard.com>
Repository: CRAN
Date/Publication: 2018-07-31 10:10:02 UTC

More information about circumplex at CRAN
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New package biglmm with initial version 0.9-1
Package: biglmm
Type: Package
Title: Bounded Memory Linear and Generalized Linear Models
Version: 0.9-1
Authors@R: c(person(given="Thomas", family="Lumley", email="tlumley@u.washington.edu", role="aut"), person(given="Christophe", family="Dutang", email="christophe.dutang@ensimag.fr", role="ctb"), person(given="Alan", family="Miller", role="ctb", comment="Algorithm AS 274"), person(given="Morven", family="Gentleman", role="ctb", comment="Algorithm AS 75"), person(given="Mark", family="Purver", email="mark_purver@hotmail.com", role="cre"))
Author: Thomas Lumley [aut], Christophe Dutang [ctb], Alan Miller [ctb] (Algorithm AS 274), Morven Gentleman [ctb] (Algorithm AS 75), Mark Purver [cre]
Maintainer: Mark Purver <mark_purver@hotmail.com>
Description: Regression for data too large to fit in memory. This package functions exactly like the 'biglm' package, but works with later versions of R.
License: GPL
Suggests: RSQLite, RODBC
Depends: DBI, methods
Enhances: leaps
Packaged: 2018-07-30 20:45:22 UTC
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2018-07-31 10:20:03 UTC
RoxygenNote: 6.0.1

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New package whitechapelR with initial version 0.2.1
Package: whitechapelR
Title: Advanced Policing Techniques for the Board Game "Letters from Whitechapel"
Version: 0.2.1
Authors@R: person("Mark", "Ewing", email = "b.mark@ewingsonline.com", role = c("aut", "cre"))
Description: Provides a set of functions to make tracking the hidden movements of the 'Jack' player easier. By tracking every possible path Jack might have traveled from the point of the initial murder including special movement such as through alleyways and via carriages, the police can more accurately narrow the field of their search. Additionally, by tracking all possible hideouts from round to round, rounds 3 and 4 should have a vastly reduced field of search.
Depends: R (>= 3.3)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: plyr, igraph
Suggests: covr, testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-30 14:31:10 UTC; u772700
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Repository: CRAN
Date/Publication: 2018-07-31 09:40:03 UTC

More information about whitechapelR at CRAN
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New package VFP with initial version 1.0
Package: VFP
Version: 1.0
Date: 2018-07-30
Title: Variance Function Program
Author: Andre Schuetzenmeister [cre, aut], Florian Dufey [aut], Andrea Geistanger [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Authors@R: c( person(given="Andre", family="Schuetzenmeister", email="andre.schuetzenmeister@roche.com", role = c("cre", "aut")), person(given="Florian", family="Dufey", email="florian.dufey@roche.com", role = c("aut")), person(given="Andrea", family="Geistanger", email="andrea.geistanger@roche.com", role = c("ctb")) )
Depends: R (>= 3.1.0), gnm
Imports: MASS, utils, stats, graphics, grDevices
Suggests: VCA, RUnit
Description: Variance function estimation for models proposed by W. Sadler in his variance function program ('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is to fit multiple variance functions to a data set and consequently assess which function reflects the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship is of great importance when individual test-results are used for defining follow-up treatment of patients.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-07-30 15:06:36 UTC; schueta6
Repository: CRAN
Date/Publication: 2018-07-31 09:40:09 UTC

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Package ordinalClust updated to version 1.3 with previous version 1.2.1 dated 2018-01-08

Title: Ordinal Data Clustering, Co-Clustering and Classification
Description: Ordinal data classification, clustering and co-clustering using model-based approach with the Bos distribution for ordinal data (Christophe Biernacki and Julien Jacques (2016) <doi:10.1007/s11222-015-9585-2>).
Author: Margot Selosse, Julien Jacques, Christophe Biernacki
Maintainer: Margot Selosse <margot.selosse@gmail.com>

Diff between ordinalClust versions 1.2.1 dated 2018-01-08 and 1.3 dated 2018-07-31

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More information about ordinalClust at CRAN
Permanent link

New package MultiFit with initial version 0.1.0
Package: MultiFit
Type: Package
Title: Multivariate Multiscale Framework for Independence Tests
Version: 0.1.0
Author: S. Gorsky, L. Ma
Maintainer: S. Gorsky <s.gorsky@duke.edu>
Description: Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky and Ma (2018) <arXiv:1806.06777>.
License: CC0
Imports: Rcpp (>= 0.12.17), data.table
LinkingTo: Rcpp, RcppArmadillo
Suggests: png, qgraph, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-30 16:15:22 UTC; hhh
Repository: CRAN
Date/Publication: 2018-07-31 09:50:09 UTC

More information about MultiFit at CRAN
Permanent link

New package jarbes with initial version 1.7.0
Package: jarbes
Type: Package
Title: Just a Rather Bayesian Evidence Synthesis
Version: 1.7.0
Date: 2018-07-30
Authors@R: c(person("Pablo Emilio", "Verde", role=c("aut","cre"), email="pabloemilio.verde@hhu.de"))
Depends: R (>= 3.4.0)
Imports: rjags (>= 3.4.0), R2jags (>= 0.04-03), stats, graphics, ggplot2, ggExtra, MASS, grid, gridExtra, mcmcplots
SystemRequirements: JAGS (>= 3.4.0) (see http://mcmc-jags.sourceforge.net)
Description: Provides a new class of Bayesian meta-analysis models that we called "The Hierarchical Meta-Regression" (HMR). The aim of HMR is to incorporate into the meta-analysis, the data collection process, which results in a model for the internal and external validity bias. In this way, it is possible to combine studies of different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS). The statistical methods and their applications are described in Verde, Ohmann, Morbach and Icks (2016) <doi:10.1002/sim.6809> and in Verde (2017) <doi:10.5772/intechopen.70231>.
License: GPL (>= 2)
Packaged: 2018-07-30 16:20:35 UTC; verde
Repository: CRAN
RoxygenNote: 6.0.1
NeedsCompilation: no
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Date/Publication: 2018-07-31 09:50:03 UTC

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New package dhh with initial version 0.0.1
Package: dhh
Title: A Heavy-Headed Distribution
Version: 0.0.1
Authors@R: person("Runlong", "Tang", email = "tangrunlong@gmail.com", role = c("aut", "cre"))
Description: The density, cumulative distribution, quantiles, and i.i.d random variables of a heavy-headed distribution. For more information, please see the vignette.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 16:36:16 UTC; rltang_dell7510
Author: Runlong Tang [aut, cre]
Maintainer: Runlong Tang <tangrunlong@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-31 09:50:06 UTC

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New package bnviewer with initial version 0.1.0
Package: bnviewer
Type: Package
Title: Interactive Visualization of Bayesian Networks
Version: 0.1.0
Depends: R (>= 3.0)
Author: Robson Fernandes
Maintainer: Robson Fernandes <robs.fernandes@outlook.com>
Description: Interactive visualization of Bayesian Networks. The 'bnviewer' package reads various structure learning algorithms provided by the 'bnlearn' package and allows you to view them interactively.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Repository: CRAN
Imports: visNetwork (>= 2.0.4), bnlearn (>= 4.3), methods, igraph (>= 1.2.1)
NeedsCompilation: no
Packaged: 2018-07-30 14:14:23 UTC; robsonfernandes
Date/Publication: 2018-07-31 09:40:07 UTC

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New package beezdemand with initial version 0.1.0
Package: beezdemand
Version: 0.1.0
Date: 2018-07-14
Title: Behavioral Economic Easy Demand
Authors@R: c(person("Brent", "Kaplan", email = "bkaplan.ku@gmail.com", role = c("aut", "cre")), person("Shawn", "Gilroy", email = "shawn.gilroy@temple.edu", role = "ctb"))
Author: Brent Kaplan [aut, cre], Shawn Gilroy [ctb]
Maintainer: Brent Kaplan <bkaplan.ku@gmail.com>
Description: Facilitates many of the analyses performed in studies of behavioral economic demand. The package supports commonly-used options for modeling operant demand including (1) data screening proposed by Stein, Koffarnus, Snider, Quisenberry, & Bickel (2015; <doi:10.1037/pha0000020>), (2) fitting models of demand such as linear (Hursh, Raslear, Bauman, & Black, 1989, <doi:10.1007/978-94-009-2470-3_22>), exponential (Hursh & Silberberg, 2008, <doi:10.1037/0033-295X.115.1.186>) and modified exponential (Koffarnus, Franck, Stein, & Bickel, 2015, <doi:10.1037/pha0000045>), and (3) calculating numerous measures relevant to applied behavioral economists (Intensity, Pmax, Omax). Also supports plotting and comparing data.
Depends: R (>= 2.5)
Imports: nlmrt, nlstools, nls2, ggplot2, reshape2, stats
Suggests: openxlsx, knitr, dplyr, tidyr, rmarkdown
License: GPL-2 | file LICENSE
URL: https://github.com/brentkaplan/beezdemand
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 17:17:24 UTC; brent
Repository: CRAN
Date/Publication: 2018-07-31 10:00:02 UTC

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Package venn updated to version 1.7 with previous version 1.6 dated 2018-05-06

Title: Draw Venn Diagrams
Description: Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set intersections.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between venn versions 1.6 dated 2018-05-06 and 1.7 dated 2018-07-31

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Package ProFound updated to version 1.1.0 with previous version 1.0.1 dated 2018-03-07

Title: Photometry Tools
Description: Core package containing all the tools for simple and advanced source extraction. This is used to create inputs for 'ProFit', or for source detection, extraction and photometry in its own right.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>

Diff between ProFound versions 1.0.1 dated 2018-03-07 and 1.1.0 dated 2018-07-31

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Package ProFit updated to version 1.2.0 with previous version 1.1.2 dated 2018-06-12

Title: Fit Projected 2D Profiles to Galaxy Images
Description: Get data / Define model / ??? / Profit! 'ProFit' is a Bayesian galaxy fitting tool that uses a fast 'C++' image generation library and a flexible interface to a large number of likelihood samplers.
Author: Aaron Robotham, Dan Taranu, Rodrigo Tobar
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>

Diff between ProFit versions 1.1.2 dated 2018-06-12 and 1.2.0 dated 2018-07-31

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Package corrr updated to version 0.3.0 with previous version 0.2.1 dated 2016-10-10

Title: Correlations in R
Description: A tool for exploring correlations. It makes it possible to easily perform routine tasks when exploring correlation matrices such as ignoring the diagonal, focusing on the correlations of certain variables against others, or rearranging and visualising the matrix in terms of the strength of the correlations.
Author: Simon Jackson [aut, cre], Jorge Cimentada [ctb], Edgar Ruiz [ctb]
Maintainer: Simon Jackson <drsimonjackson@gmail.com>

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Package janitor updated to version 1.1.1 with previous version 1.1.0 dated 2018-07-18

Title: Simple Tools for Examining and Cleaning Dirty Data
Description: The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and isolate duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness. Advanced R users can already do everything covered here, but with janitor they can do it faster and save their thinking for the fun stuff.
Author: Sam Firke [aut, cre], Chris Haid [ctb], Ryan Knight [ctb], Bill Denney [ctb]
Maintainer: Sam Firke <samuel.firke@gmail.com>

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More information about janitor at CRAN
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