Tue, 20 Jun 2017

Package taxizedb updated to version 0.1.4 with previous version 0.1.0 dated 2017-05-03

Title: Tools for Working with 'Taxonomic' Databases
Description: Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

Diff between taxizedb versions 0.1.0 dated 2017-05-03 and 0.1.4 dated 2017-06-20

 DESCRIPTION                       |   14 +++---
 MD5                               |   24 +++++-----
 NAMESPACE                         |   10 +++-
 NEWS.md                           |   10 ++++
 R/db_load.R                       |   58 ++++++++++++++-----------
 R/src.R                           |   25 +++++++----
 R/taxizedb-package.R              |    8 ++-
 R/zzz.R                           |   16 +++----
 README.md                         |   85 ++++++++++++++++----------------------
 man/db_load.Rd                    |   13 ++---
 man/src_taxizedb.Rd               |    7 +--
 tests/testthat/test-sql_collect.R |    4 -
 tests/testthat/test-src.R         |    8 +--
 13 files changed, 150 insertions(+), 132 deletions(-)

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Package rkafkajars updated to version 1.1 with previous version 1.0 dated 2015-04-10

Title: External Jars Required for Package 'rkafka'
Description: The 'rkafkajars' package collects all the external jars required for the 'rkafka' package.
Author: Shruti Gupta [aut,cre], Coda Hale and Yammer Inc.[ctb,cph],Sun Microsystems Inc.[ctb,cph],Marc Prud'hommeaux[ctb,cph],Paul Holser[ctb],Junit[ctb,cph],The Apache Software Foundation [ctb,cph],Stefan Groschupf[ctb,cph],Taro L.Saito[ctb],EPFL Typesafe Inc.[ctb,cph],QOS.ch[ctb,cph]
Maintainer: Shruti Gupta <shrutigupta34@gmail.com>

Diff between rkafkajars versions 1.0 dated 2015-04-10 and 1.1 dated 2017-06-20

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

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Package RcppCCTZ updated to version 0.2.3 with previous version 0.2.2 dated 2017-04-21

Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppCCTZ versions 0.2.2 dated 2017-04-21 and 0.2.3 dated 2017-06-20

 RcppCCTZ-0.2.2/RcppCCTZ/src/init.c                  |only
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 RcppCCTZ-0.2.3/RcppCCTZ/R/init.R                    |    7 ++---
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 RcppCCTZ-0.2.3/RcppCCTZ/inst/NEWS.Rd                |   11 +++++++
 RcppCCTZ-0.2.3/RcppCCTZ/src/RcppExports.cpp         |   23 ++++++++++++++++
 RcppCCTZ-0.2.3/RcppCCTZ/src/time_tool.cc            |    2 +
 RcppCCTZ-0.2.3/RcppCCTZ/src/utilities.cpp           |   10 ++-----
 RcppCCTZ-0.2.3/RcppCCTZ/tests/simpleTests.Rout.save |    7 ++---
 12 files changed, 100 insertions(+), 43 deletions(-)

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Package qdapTools updated to version 1.3.3 with previous version 1.3.1 dated 2015-09-25

Title: Tools for the 'qdap' Package
Description: A collection of tools associated with the 'qdap' package that may be useful outside of the context of text analysis.
Author: Bryan Goodrich [ctb], Dason Kurkiewicz [ctb], Kirill Muller [ctb], Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>

Diff between qdapTools versions 1.3.1 dated 2015-09-25 and 1.3.3 dated 2017-06-20

 DESCRIPTION                   |    9 +++--
 MD5                           |   54 ++++++++++++++++-----------------
 NAMESPACE                     |    2 -
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 inst/CITATION                 |    4 +-
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 tests/testthat/test-hms2sec.R |    2 -
 28 files changed, 257 insertions(+), 250 deletions(-)

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New package POMaSPU with initial version 1.0.0
Package: POMaSPU
Type: Package
Title: Adaptive Association Tests for Multiple Phenotypes using Proportional Odds Model (POM-aSPU)
Version: 1.0.0
Date: 2017-06-20
Author: Junghi Kim and Wei Pan
Maintainer: Junghi Kim <junghikim0@gmail.com>
Description: POM-aSPU test evaluates an association between an ordinal response and multiple phenotypes, for details see Kim and Pan (2017) <DOI:10.1002/gepi.22033>.
License: GNU General Public License (>= 3)
Depends: R (>= 2.10), MASS, matrixStats, stats
Imports: Rcpp (>= 0.12.6)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-06-20 21:01:49 UTC; jkim30
Repository: CRAN
Date/Publication: 2017-06-20 23:03:47 UTC

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New package PeakSegDP with initial version 2017.06.20
Package: PeakSegDP
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Author: Toby Dylan Hocking, Guillem Rigaill
Version: 2017.06.20
License: GPL-3
Title: Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data
Description: A quadratic time dynamic programming algorithm can be used to compute an approximate solution to the problem of finding the most likely changepoints with respect to the Poisson likelihood, subject to a constraint on the number of segments, and the changes which must alternate: up, down, up, down, etc. For more info read <http://proceedings.mlr.press/v37/hocking15.html> "PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data" by TD Hocking et al, proceedings of ICML2015.
Suggests: ggplot2 (>= 2.0), testthat, penaltyLearning
Depends: R (>= 2.10)
NeedsCompilation: yes
Packaged: 2017-06-20 19:14:51 UTC; thocking
Repository: CRAN
Date/Publication: 2017-06-20 23:23:02 UTC

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

Title: Bayesian Network Structure Learning
Description: From a given data frame, this package learns its Bayesian network structure based on a selected score.
Author: Joe Suzuki and Jun Kawahara
Maintainer: Joe Suzuki <j-suzuki@sigmath.es.osaka-u.ac.jp>

Diff between BNSL versions 0.1.1 dated 2017-06-20 and 0.1.2 dated 2017-06-20

 DESCRIPTION        |    8 ++++----
 MD5                |    4 ++--
 src/parent_set.cpp |    5 +++++
 3 files changed, 11 insertions(+), 6 deletions(-)

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Package BDgraph updated to version 2.38 with previous version 2.37 dated 2017-05-24

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889> and Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>

Diff between BDgraph versions 2.37 dated 2017-05-24 and 2.38 dated 2017-06-20

 DESCRIPTION            |    8 
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 NEWS                   |    5 
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 src/copula.cpp         |   71 +++----
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 src/gm_mpl_bd_dis.cpp  |   30 ++-
 src/init.c             |    4 
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 34 files changed, 738 insertions(+), 552 deletions(-)

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Package congressbr updated to version 0.1.1 with previous version 0.1.0 dated 2017-04-30

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 Myles McDonnell, Guilherme Jardim Duarte and Danilo Freire
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>

Diff between congressbr versions 0.1.0 dated 2017-04-30 and 0.1.1 dated 2017-06-20

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Package nonmem2R updated to version 0.1.7 with previous version 0.1.5 dated 2016-10-25

Title: Loading NONMEM Output Files and Simulate with Parameter Uncertainty
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/solutions/nonmem/> ) output files and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>

Diff between nonmem2R versions 0.1.5 dated 2016-10-25 and 0.1.7 dated 2017-06-20

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 NAMESPACE            |    3 
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Package eulerr updated to version 2.0.0 with previous version 1.1.0 dated 2017-02-05

Title: Area-Proportional Euler Diagrams
Description: If possible, generates exactly area-proportional Euler diagrams, or otherwise approximately proportional diagrams using numerical optimization. A Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented.
Author: Johan Larsson [aut, cre], A. Jonathan R. Godfrey [ctb]
Maintainer: Johan Larsson <johanlarsson@outlook.com>

Diff between eulerr versions 1.1.0 dated 2017-02-05 and 2.0.0 dated 2017-06-20

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New package rcoreoa with initial version 0.1.0
Package: rcoreoa
Type: Package
Title: Client for the CORE API
Description: Client for the CORE API (<https://core.ac.uk/docs/>). CORE (<https://core.ac.uk>) aggregates open access research outputs from repositories and journals worldwide and make them available to the public.
Version: 0.1.0
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus+r@gmail.com"), person("Aristotelis", "Charalampous", role = "ctb"), person("Simon", "Goring", role = "ctb") )
License: MIT + file LICENSE
URL: https://github.com/ropensci/rcoreoa
BugReports: https://github.com/ropensci/rcoreoa/issues
VignetteBuilder: knitr
Imports: crul (>= 0.3.8), jsonlite (>= 1.5), pdftools (>= 1.3)
Suggests: roxygen2 (>= 6.0.1), testthat, knitr, rmarkdown, rcrossref
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-20 18:35:38 UTC; sacmac
Author: Scott Chamberlain [aut, cre], Aristotelis Charalampous [ctb], Simon Goring [ctb]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-20 19:01:56 UTC

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New package mssqlR with initial version 1.0.0
Package: mssqlR
Title: MSSQL Querying using R
Version: 1.0.0
Authors@R: person("Abhishek", "Sinha", email = "abhishek.sparta@gmail.com", role = c("aut", "cre"))
Description: Can be used to query data from data from Microsoft SQL Server (MSSQL, see <http://www.microsoft.com/sqlserver/> for more information). Based on the concepts of Entity Framework, the package allows querying data from MSSQL Database.
Depends: R (>= 3.4.0)
License: GPL (>= 3) | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: RODBC, magrittr
RoxygenNote: 6.0.1.9000
Maintainer: Abhishek Sinha <abhishek.sparta@gmail.com>
NeedsCompilation: no
Packaged: 2017-06-20 18:05:20 UTC; abhishek
Author: Abhishek Sinha [aut, cre]
Repository: CRAN
Date/Publication: 2017-06-20 19:03:11 UTC

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Package mlt updated to version 0.2-0 with previous version 0.1-3 dated 2017-04-05

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach described in Hothorn et al. (2016) <arXiv:1508.06749>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt versions 0.1-3 dated 2017-04-05 and 0.2-0 dated 2017-06-20

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 MD5                     |   24 ++++++++++++------------
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Package distillery updated to version 1.0-4 with previous version 1.0-2 dated 2015-07-24

Title: Method Functions for Confidence Intervals and to Distill Information from an Object
Description: Some very simple method functions for confidence interval calculation, bootstrap resampling, and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>

Diff between distillery versions 1.0-2 dated 2015-07-24 and 1.0-4 dated 2017-06-20

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Package arfima updated to version 1.4-0 with previous version 1.3-4 dated 2015-12-31

Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time series, possibly mixed with ARMA, regression, transfer-function components. Exact methods (MLE, forecasting, simulation) are used.
Author: JQ (Justin) Veenstra [aut, cre], A.I. McLeod [aut]
Maintainer: JQ (Justin) Veenstra <jqveenstra@gmail.com>

Diff between arfima versions 1.3-4 dated 2015-12-31 and 1.4-0 dated 2017-06-20

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Package scape updated to version 2.3-1 with previous version 2.2-0 dated 2014-03-12

Title: Statistical Catch-at-Age Plotting Environment
Description: Import, plot, and diagnose results from statistical catch-at-age models, used in fisheries stock assessment.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>

Diff between scape versions 2.2-0 dated 2014-03-12 and 2.3-1 dated 2017-06-20

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 68 files changed, 5149 insertions(+), 5008 deletions(-)

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New package nmaINLA with initial version 0.1.0
Package: nmaINLA
Type: Package
Title: Network Meta-Analysis using Integrated Nested Laplace Approximations
Version: 0.1.0
Date: 2017-06-20
Authors@R: c( person("Burak Kuersad", "Guenhan", email = "burak.gunhan@med.uni-goettingen.de", role = c("aut", "cre")))
Description: Performs network meta-analysis using integrated nested Laplace approximations ('INLA'). Includes methods to assess the heterogeneity and inconsistency in the network. Contains more than ten different network meta-analysis data. Installation of R package 'INLA' is compulsory for successful usage. 'INLA' package can be obtained from <http://www.r-inla.org>. We recommend the testing version.
License: GPL (>= 2)
LazyData: TRUE
Depends: R (>= 2.10)
Additional_repositories: http://www.math.ntnu.no/inla/R/testing
RoxygenNote: 6.0.1
Suggests: INLA, knitr, testthat
VignetteBuilder: knitr
URL: http://github.com/gunhanb/nmaINLA
BugReports: http://github.com/gunhanb/nmaINLA/issues
NeedsCompilation: no
Packaged: 2017-06-20 17:46:03 UTC; gunhan
Author: Burak Kuersad Guenhan [aut, cre]
Maintainer: Burak Kuersad Guenhan <burak.gunhan@med.uni-goettingen.de>
Repository: CRAN
Date/Publication: 2017-06-20 18:04:02 UTC

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New package ukbabynames with initial version 0.1.1
Package: ukbabynames
Title: UK Baby Names Data
Version: 0.1.1
Authors@R: c( person("Thomas J.", "Leeper", , "thosjleeper@gmail.com", c("aut", "cre")) )
Description: Full listing of UK baby names occurring more than three times per year between 1996 and 2015, and rankings of baby name popularity by decade from 1904 to 1994.
Depends: R (>= 2.10)
License: CC0
LazyData: true
URL: http://github.com/leeper/ukbabynames
BugReports: https://github.com/leeper/ukbabynames/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-20 16:03:08 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-20 17:20:15 UTC

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New package swapClass with initial version 1.0
Package: swapClass
Type: Package
Title: A Null Model Adapted to Abundance Class Data in Ecology
Version: 1.0
Date: 2017-06-20
Author: Benjamin Borgy, Remi Perronne, Xavier Reboud
Maintainer: Benjamin Borgy <benjamin.borgy@gmail.com>
Depends: R (>= 3.1.1), inline, utils, methods
Description: A null model randomizing semi-quantitative multi-classes (or ordinal) data by swapping sub-matrices while both the row and the column marginal sums are held constant.
License: GPL-3
NeedsCompilation: no
Packaged: 2017-06-20 16:00:20 UTC; jfb
Repository: CRAN
Date/Publication: 2017-06-20 17:20:45 UTC

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New package rematch2 with initial version 2.0.1
Package: rematch2
Title: Tidy Output from Regular Expression Matching
Version: 2.0.1
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Description: Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/r-lib/rematch2#readme
BugReports: https://github.com/r-lib/rematch2/issues
RoxygenNote: 6.0.1
Imports: tibble
Suggests: covr, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2017-06-20 15:38:29 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2017-06-20 17:21:11 UTC

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Package gmt updated to version 2.0-0 with previous version 1.2-0 dated 2014-03-12

Title: Interface Between GMT Map-Making Software and R
Description: Interface between the GMT map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The gmt package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>

Diff between gmt versions 1.2-0 dated 2014-03-12 and 2.0-0 dated 2017-06-20

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Package learnr updated to version 0.9 with previous version 0.8 dated 2017-05-08

Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.
Author: JJ Allaire [aut, cre], RStudio, Inc. [cph], Ajax.org B.V. [ctb, cph] (Ace library), Zeno Rocha [ctb, cph] (clipboard.js library), Nick Payne [ctb, cph] (Bootbox library), Julie Cameron [ctb] (SlickQuiz library), Quicken Loans [cph] (SlickQuiz library), Mozilla [ctb, cph] (localforage library)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between learnr versions 0.8 dated 2017-05-08 and 0.9 dated 2017-06-20

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 NAMESPACE                                 |    4 
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New package tukeytrend with initial version 0.4
Package: tukeytrend
Type: Package
Version: 0.4
Title: Tukeys Trend Test via Multiple Marginal Models
Date: 2017-06-20
Authors@R: c(person("Frank","Schaarschmidt", role=c("aut","cre"), email="schaarschmidt@biostat.uni-hannover.de"), person("Christian", "Ritz", role="aut"), person("Ludwig", "Hothorn", role="ctb"))
Author: Frank Schaarschmidt [aut, cre], Christian Ritz [aut], Ludwig Hothorn [ctb]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Depends: multcomp
Imports: stats, pbkrtest, mgcv, lme4, nlme, Matrix
Suggests: knitr, ggplot2, gridExtra, xtable, reshape2, sandwich, stepp, aods3, CorrBin, SASmixed, SimComp, HSAUR3
VignetteBuilder: knitr
Description: Provides wrapper functions to the multiple marginal model function mmm() of package 'multcomp' to implement the trend test of Tukey, Ciminera and Heyse (1985) <DOI:10.2307/2530666> for general parametric models.
License: GPL-2
NeedsCompilation: no
Packaged: 2017-06-20 09:20:45 UTC; Schaarschmidt
Repository: CRAN
Date/Publication: 2017-06-20 15:51:58 UTC

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New package tidycensus with initial version 0.1.2
Package: tidycensus
Type: Package
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Version: 0.1.2
Authors@R: c(person(given="Kyle", family="Walker", email="kyle.walker@tcu.edu", role=c("aut", "cre")))
Date: 2017-06-19
URL: https://github.com/walkerke/tidycensus
BugReports: https://github.com/walkerke/tidycensus/issues
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many geographies.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: httr, sf, dplyr, tigris, stringr, jsonlite, purrr, rvest, tidyr, rappdirs, readr, xml2, units
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-20 11:31:45 UTC; KyleWalker
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Repository: CRAN
Date/Publication: 2017-06-20 15:43:45 UTC

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Package StatCharrms updated to version 0.90.4 with previous version 0.90.3 dated 2017-05-16

Title: Statistical Analysis of Chemistry, Histopathology, and Reproduction Endpoints Including Repeated Measures and Multi-Generation Studies
Description: A front end for the statistical analyses involved in the tier II endocrine disruptor screening program. The analyses available to this package are: Rao-Scott adjusted Cochran-Armitage test for trend By Slices (RSCABS), a Standard Cochran-Armitage test for trend By Slices (SCABS), mixed effects Cox proportional model, Jonckheere-Terpstra step down trend test Dunn test, one way ANOVA, weighted ANOVA, mixed effects ANOVA, repeated measures ANOVA, and Dunnett test.
Author: Joe Swintek [aut, cre], Kevin Flynn [ctb], Jon Haselman [ctb]
Maintainer: Joe Swintek <swintek.joe@epa.gov>

Diff between StatCharrms versions 0.90.3 dated 2017-05-16 and 0.90.4 dated 2017-06-20

 DESCRIPTION              |   10 +++++-----
 MD5                      |    8 ++++----
 R/Run.StatCharrms.R      |   18 +++++++++---------
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 5 files changed, 21 insertions(+), 21 deletions(-)

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New package SFS with initial version 0.1
Package: SFS
Type: Package
Title: Similarity-First Search Seriation Algorithm
Version: 0.1
Date: 2017-06-16
Authors@R: c( person("Matteo", "Seminaroti", role = c("aut", "cph"), email = "matteo.seminaroti@gmail.com"), person("Utz-Uwe", "Haus", role = c("aut", "cre", "cph"), email = "uhaus@cray.com"))
Maintainer: Utz-Uwe Haus <uhaus@cray.com>
Description: An implementation of the Similarity-First Search algorithm (SFS), a combinatorial algorithm which can be used to solve the seriation problem and to recognize some structured weighted graphs. The SFS algorithm represents a generalization to weighted graphs of the graph search algorithm Lexicographic Breadth-First Search (Lex-BFS), a variant of Breadth-First Search. The SFS algorithm reduces to Lex-BFS when applied to binary matrices (or, equivalently, unweighted graphs). Hence this library can be also considered for Lex-BFS applications such as recognition of graph classes like chordal or unit interval graphs. In fact, the SFS seriation algorithm implemented in this package is a multisweep algorithm, which consists in repeating a finite number of SFS iterations (at most \eqn{n} sweeps for a matrix of size \eqn{n}). If the data matrix has a Robinsonian structure, then the ranking returned by the multistep SFS algorithm is a Robinson ordering of the input matrix. Otherwise the algorithm can be used as a heuristic to return a ranking partially satisfying the Robinson property.
License: GPL-3
Encoding: UTF-8
Imports: Rcpp (>= 0.12.7)
Suggests: seriation
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-06-20 08:53:02 UTC; uhaus
Author: Matteo Seminaroti [aut, cph], Utz-Uwe Haus [aut, cre, cph]
Repository: CRAN
Date/Publication: 2017-06-20 15:52:38 UTC

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Package RxnSim updated to version 1.0.2 with previous version 1.0.1 dated 2015-04-08

Title: Functions to Compute Chemical Reaction Similarity
Description: Methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages 'rCDK' and 'fingerprint' for cheminformatics functionality.
Author: Varun Giri [aut, cre]
Maintainer: Varun Giri <varungiri@gmail.com>

Diff between RxnSim versions 1.0.1 dated 2015-04-08 and 1.0.2 dated 2017-06-20

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Package red updated to version 1.1.0 with previous version 1.0.1 dated 2017-04-12

Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <http://www.iucn.org> for more information) red list criteria.
Author: Pedro Cardoso
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>

Diff between red versions 1.0.1 dated 2017-04-12 and 1.1.0 dated 2017-06-20

 DESCRIPTION     |   10 ++---
 MD5             |   13 ++++---
 NAMESPACE       |    1 
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 man/map.sdm.Rd  |    4 +-
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Package ranger updated to version 0.8.0 with previous version 0.7.0 dated 2017-03-31

Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package 'GenABEL') can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <cran@wrig.de>

Diff between ranger versions 0.7.0 dated 2017-03-31 and 0.8.0 dated 2017-06-20

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 ranger-0.8.0/ranger/NAMESPACE                                |    1 
 ranger-0.8.0/ranger/NEWS                                     |    6 
 ranger-0.8.0/ranger/R/RcppExports.R                          |    4 
 ranger-0.8.0/ranger/R/csrf.R                                 |    1 
 ranger-0.8.0/ranger/R/formula.R                              |    5 
 ranger-0.8.0/ranger/R/getTerminalNodeIDs.R                   |    1 
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Package mlt.docreg updated to version 0.2-0 with previous version 0.1-5 dated 2017-04-05

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt.docreg versions 0.1-5 dated 2017-04-05 and 0.2-0 dated 2017-06-20

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New package geofacet with initial version 0.1.4
Package: geofacet
Title: 'ggplot2' Faceting Utilities for Geographical Data
Version: 0.1.4
Authors@R: person("Ryan", "Hafen", email = "rhafen@gmail.com", role = c("aut", "cre"))
Description: Provides geofaceting functionality for 'ggplot2'. Geofaceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Depends: R (>= 3.3.2)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, gtable, graphics
Suggests: testthat, covr, lintr, knitr, rmarkdown, packagedocs
RoxygenNote: 6.0.1
VignetteBuilder: knitr, packagedocs
NeedsCompilation: no
Packaged: 2017-06-20 15:32:24 UTC; hafen
Author: Ryan Hafen [aut, cre]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-20 15:49:38 UTC

More information about geofacet at CRAN
Permanent link

Package apaTables updated to version 1.5.1 with previous version 1.5.0 dated 2017-03-25

Title: Create American Psychological Association (APA) Style Tables
Description: A common task faced by researchers is the creation of APA style (i.e., American Psychological Association style) tables from statistical output. In R a large number of function calls are often needed to obtain all of the desired information for a single APA style table. As well, the process of manually creating APA style tables in a word processor is prone to transcription errors. This package creates Word files (.doc files) containing APA style tables for several types of analyses. Using this package minimizes transcription errors and reduces the number commands needed by the user.
Author: David Stanley [aut, cre]
Maintainer: David Stanley <dstanley@uoguelph.ca>

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Package rpostgisLT updated to version 0.5.0 with previous version 0.4.0 dated 2016-11-01

Title: Managing Animal Movement Data with 'PostGIS' and R
Description: Integrates R and the 'PostgreSQL/PostGIS' database system to build and manage animal trajectory (movement) data sets. The package relies on 'ltraj' objects from the R package 'adehabitatLT', building the analogous 'pgtraj' data structure in 'PostGIS'. Functions allow users to seamlessly transfer between 'ltraj' and 'pgtraj', as well as build new 'pgtraj' directly from location data stored in the database.
Author: Balázs Dukai [aut] (Package creator during Google Summer of Code 2016), Mathieu Basille [aut], David Bucklin [aut, cre], Clément Calenge [ctb]
Maintainer: David Bucklin <dbucklin@ufl.edu>

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Package antaresViz updated to version 0.10 with previous version 0.9 dated 2017-06-01

Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations.
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between antaresViz versions 0.9 dated 2017-06-01 and 0.10 dated 2017-06-20

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Package questionr updated to version 0.6.1 with previous version 0.6.0 dated 2017-03-21

Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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Package quantmod updated to version 0.4-10 with previous version 0.4-9 dated 2017-05-29

Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, aut], Wouter Thielen [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>

Diff between quantmod versions 0.4-9 dated 2017-05-29 and 0.4-10 dated 2017-06-20

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Package Compind updated to version 1.2 with previous version 1.1.2 dated 2016-06-27

Title: Composite Indicators Functions
Description: Contains several functions to enhance approaches to the Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps.
Author: Francesco Vidoli, Elisa Fusco
Maintainer: Francesco Vidoli <fvidoli@gmail.com>

Diff between Compind versions 1.1.2 dated 2016-06-27 and 1.2 dated 2017-06-20

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Package WeightedCluster updated to version 1.2-1 with previous version 1.2 dated 2014-01-16

Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting clusters of state sequences.
Author: Matthias Studer [aut, cre]
Maintainer: Matthias Studer <matthias.studer@unige.ch>

Diff between WeightedCluster versions 1.2 dated 2014-01-16 and 1.2-1 dated 2017-06-20

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Package mgm updated to version 1.2-1 with previous version 1.2-0 dated 2017-05-26

Title: Estimating Time-Varying k-Order Mixed Graphical Models
Description: Estimation of k-Order time-varying Mixed Graphical Models and mixed VAR(p) models via elastic-net regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>

Diff between mgm versions 1.2-0 dated 2017-05-26 and 1.2-1 dated 2017-06-20

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Package edeaR updated to version 0.6.0 with previous version 0.5.0 dated 2017-04-01

Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Functions for exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Gert Janssenswillen [aut, cre], Marijke Swennen [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>

Diff between edeaR versions 0.5.0 dated 2017-04-01 and 0.6.0 dated 2017-06-20

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More information about edeaR at CRAN
Permanent link

Package spant updated to version 0.3.0 with previous version 0.2.0 dated 2017-05-24

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data.
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

Diff between spant versions 0.2.0 dated 2017-05-24 and 0.3.0 dated 2017-06-20

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More information about spant at CRAN
Permanent link

Package leaflet.minicharts updated to version 0.4.0 with previous version 0.3.1 dated 2017-05-30

Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with package 'leaflet'. These charts can be used to represent at same time multiple variables on a single map.
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between leaflet.minicharts versions 0.3.1 dated 2017-05-30 and 0.4.0 dated 2017-06-20

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More information about leaflet.minicharts at CRAN
Permanent link

Package LBSPR updated to version 0.1.1 with previous version 0.1.0 dated 2016-12-13

Title: Length-Based Spawning Potential Ratio
Description: Simulate expected equilibrium length composition, YPR, and SPR using the LBSPR model. Fit the LBSPR model to length data to estimate selectivity, relative fishing mortality, and spawning potential ratio for data-limited fisheries.
Author: Adrian Hordyk [aut, cre]
Maintainer: Adrian Hordyk <ar.hordyk@gmail.com>

Diff between LBSPR versions 0.1.0 dated 2016-12-13 and 0.1.1 dated 2017-06-20

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 59 files changed, 1092 insertions(+), 678 deletions(-)

More information about LBSPR at CRAN
Permanent link

Package SemiParBIVProbit updated to version 3.8-2 with previous version 3.8-1 dated 2017-01-18

Title: Semiparametric Copula Regression Models
Description: Routines for fitting various copula regression models, with several types of covariate effects, in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>

Diff between SemiParBIVProbit versions 3.8-1 dated 2017-01-18 and 3.8-2 dated 2017-06-20

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 SemiParBIVProbit-3.8-2/SemiParBIVProbit/R/copgHsCont.r                  | 1857 +++++++++-
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More information about SemiParBIVProbit at CRAN
Permanent link

New package RLeafAngle with initial version 1.0
Package: RLeafAngle
Type: Package
Title: Estimates, Plots and Evaluates Leaf Angle Distribution Functions, Calculates Extinction Coefficients
Version: 1.0
Date: 2017-6-19
Author: Wei-Min Wang <wmwang@gmail.com>
Maintainer: Wei-Min Wang <wmwang@gmail.com>
Description: Leaf angle distribution is described by a number of functions (e.g. ellipsoidal, Beta and rotated ellipsoidal). The parameters of leaf angle distributions functions are estimated through different empirical relationship. This package includes estimations of parameters of different leaf angle distribution function, plots and evaluates leaf angle distribution functions, calculates extinction coefficients given leaf angle distribution. Reference: Wang(2007)<doi:10.1016/j.agrformet.2006.12.003>.
License: GPL
Imports: stats
Depends:
Suggests:
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-20 01:23:08 UTC; Administrator
Repository: CRAN
Date/Publication: 2017-06-20 06:29:21 UTC

More information about RLeafAngle at CRAN
Permanent link

Package DepthProc updated to version 2.0.1 with previous version 1.0.7 dated 2016-02-12

Title: Statistical Depth Functions for Multivariate Analysis
Description: Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Author: Zygmunt Zawadzki [aut, cre], Daniel Kosiorowski [aut], Krzysztof Slomczynski [ctb], Mateusz Bocian [ctb], Anna Wegrzynkiewicz [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

Diff between DepthProc versions 1.0.7 dated 2016-02-12 and 2.0.1 dated 2017-06-20

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 DepthProc-2.0.1/DepthProc/man/plot-BinnDepth2d-ANY-method.Rd    |   10 
 DepthProc-2.0.1/DepthProc/man/plot-DepthDensity-ANY-method.Rd   |   10 
 DepthProc-2.0.1/DepthProc/man/plot-LSDepthContour-ANY-method.Rd |   16 
 DepthProc-2.0.1/DepthProc/man/plot-methods.Rd                   |   14 
 DepthProc-2.0.1/DepthProc/man/runifsphere.Rd                    |   10 
 DepthProc-2.0.1/DepthProc/man/scaleCurve.Rd                     |   52 
 DepthProc-2.0.1/DepthProc/man/trimProjReg2d.Rd                  |   78 -
 DepthProc-2.0.1/DepthProc/man/under5.mort.Rd                    |    4 
 DepthProc-2.0.1/DepthProc/src/Depth.cpp                         |  140 +-
 DepthProc-2.0.1/DepthProc/src/Makevars                          |    1 
 DepthProc-2.0.1/DepthProc/src/Makevars.win                      |    1 
 DepthProc-2.0.1/DepthProc/src/RcppExports.cpp                   |  126 +
 DepthProc-2.0.1/DepthProc/src/UtilsCPP.cpp                      |   63 
 DepthProc-2.0.1/DepthProc/src/depthcpp.cpp                      |   21 
 DepthProc-2.0.1/DepthProc/src/init.c                            |only
 DepthProc-2.0.1/DepthProc/tests                                 |only
 117 files changed, 3447 insertions(+), 3120 deletions(-)

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New package BNSL with initial version 0.1.1
Package: BNSL
Type: Package
Title: Bayesian Network Structure Learning
Version: 0.1.1
Date: 2017-03-03
Author: Joe Suzuki and Jun Kawahara
Maintainer: Joe Suzuki <j-suzuki@sigmath.es.osaka-u.ac.jp>
Depends: bnlearn, igraph
Description: From a given data frame, this package learns its Bayesian network structure based on a selected score.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.0)
LinkingTo: Rcpp
Packaged: 2017-06-19 23:57:08 UTC; Prof-Joe
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2017-06-20 06:47:13 UTC

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Package anchoredDistr updated to version 1.0.3 with previous version 1.0.2 dated 2017-06-15

Title: Post-Processing for the Method of Anchored Distributions
Description: Supplements the 'MAD#' software (see <http://mad.codeplex.com/>, or Osorio-Murillo, et al. (2015) <doi:10.1016/j.envsoft.2015.01.002>) that implements the Method of Anchored Distributions for inferring geostatistical parameters (see Rubin, et al. (2010) <doi:10.1029/2009WR008799>). Reads 'MAD#' result databases, performs dimension reduction on inversion data, calculates likelihoods and posteriors, and tests for convergence. Also generates plots to summarize results.
Author: Heather Savoy
Maintainer: Heather Savoy <frystacka@berkeley.edu>

Diff between anchoredDistr versions 1.0.2 dated 2017-06-15 and 1.0.3 dated 2017-06-20

 DESCRIPTION                            |   14 +-
 MD5                                    |  160 +++++++++++++++++++++++++++++++--
 NAMESPACE                              |    3 
 R/readMAD.R                            |    8 +
 inst/doc/anchoredDistr.R               |    9 -
 inst/doc/anchoredDistr.Rmd             |   11 --
 inst/doc/anchoredDistr.html            |   12 +-
 inst/extdata/Tutorial_example1.xResult |only
 inst/extdata/example1                  |only
 vignettes/anchoredDistr.Rmd            |   11 --
 10 files changed, 184 insertions(+), 44 deletions(-)

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