Sun, 29 Jan 2017

New package statip with initial version 0.1.4
Package: statip
Type: Package
Title: Miscellaneous Basic Statistical Functions
Version: 0.1.4
Date: 2017-01-26
Authors@R: c(person("Paul", "Poncet", , "paulponcet@yahoo.fr", role = c("aut", "cre")), person("The R Core Team", role = c("aut", "cph"), comment = "C function 'BinDist' copied from package 'stats'"), person("The R Foundation", role = "cph", comment = "C function 'BinDist' copied from package 'stats'"), person("Adrian", "Baddeley", role = "ctb", comment = "C function 'BinDist' copied from package 'stats'"))
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().
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.1.3)
Imports: bazar, dplyr, graphics, stats
Suggests: knitr, testthat
URL: https://github.com/paulponcet/statip
BugReports: https://github.com/paulponcet/statip/issues
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2017-01-28 22:29:12 UTC; YL1101
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>
Repository: CRAN
Date/Publication: 2017-01-29 22:01:45

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New package observer with initial version 0.1.2
Package: observer
Type: Package
Title: Observe and Check your Data
Version: 0.1.2
Date: 2017-01-25
Authors@R: person("Paul", "Poncet", , "paulponcet@yahoo.fr", role = c("aut", "cre"))
Description: Checks that a given dataset passes user-specified rules. The main functions are observe_if() and inspect().
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.1.3)
Imports: bazar, bit, dplyr, lazyeval, magrittr, tibble, utils
VignetteBuilder: knitr
Suggests: knitr, ggplot2, testthat
URL: https://github.com/paulponcet/observer
BugReports: https://github.com/paulponcet/observer/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-29 20:23:34 UTC; YL1101
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Repository: CRAN
Date/Publication: 2017-01-29 22:03:43

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New package nzpullover with initial version 0.0.2
Package: nzpullover
Title: Driving Offences in New Zealand Between 2009 and 2016
Version: 0.0.2
Authors@R: person("Duncan", "Garmonsway", email = "nacnudus@gmail.com", role = c("aut", "cre"))
Description: Datasets of driving offences and fines in New Zealand between 2009 and 2016. Originally published by the New Zealand Police at <http://www.police.govt.nz/about-us/publication/road-policing-driver-offence-data-january-2009-september-2016>.
Depends: R (>= 3.2.5)
License: CC0
Encoding: UTF-8
LazyData: true
URL: https://github.com/nacnudus/nzpullover
BugReports: https://github.com/nacnudus/nzpullover/issues
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2017-01-29 18:22:15 UTC; nacnudus
Author: Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Repository: CRAN
Date/Publication: 2017-01-29 21:33:21

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New package vistime with initial version 0.1.0
Package: vistime
Title: Interactive R Timelines using 'plotly.js'
Version: 0.1.0
Date: 2017-02-01
Authors@R: person( "Sandro", "Raabe" , role = c("aut", "cre") , email = "shosaco_nospam@hotmail.com" )
Maintainer: Sandro Raabe <shosaco_nospam@hotmail.com>
Description: Create fully interactive time lines or Gantt charts using 'plotly.js'. The charts can be included in Shiny apps and manipulated via 'plotly_build()'.
License: GPL-3 | file LICENSE
URL: https://github.com/shosaco/vistime
BugReports: https://github.com/shosaco/vistime/issues
Depends: R (>= 3.1.0)
Imports: plotly (>= 4.5.2), RColorBrewer (>= 1.1.2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-29 16:17:12 UTC; d90862
Author: Sandro Raabe [aut, cre]
Repository: CRAN
Date/Publication: 2017-01-29 17:35:45

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Package TTCA updated to version 0.1.1 with previous version 0.1.0 dated 2016-06-20

Title: Transcript Time Course Analysis
Description: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Paper: Albrecht, Marco, et al. (2017)<DOI:10.1186/s12859-016-1440-8>.
Author: Marco Albrecht
Maintainer: Marco Albrecht <marco.albrecht@posteo.de>

Diff between TTCA versions 0.1.0 dated 2016-06-20 and 0.1.1 dated 2017-01-29

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Package SimInf updated to version 3.0.0 with previous version 2.0.0 dated 2016-05-04

Title: A Framework for Data-Driven Stochastic Disease Spread Simulations
Description: Livestock movements are important for the spread of many infectious diseases between herds. The package provides an efficient and flexible framework for stochastic disease spread modelling that integrates within-herd disease dynamics as continuous-time Markov chains and livestock movements between herds as scheduled events. The core simulation solver is implemented in C and uses 'OpenMP' (if available) to divide work over multiple processors. The package contains template models and can be extended with user defined models.
Author: Stefan Widgren (National Veterinary Institute, Sweden), Pavol Bauer (Uppsala University, Sweden), Stefan Engblom (Uppsala University, Sweden)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

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Package statoo (with last version 0.1.3) was removed from CRAN

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

2017-01-27 0.1.3

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Package geocodeHERE (with last version 0.1.3) was removed from CRAN

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

2015-07-15 0.1.3
2015-03-04 0.1.2

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Package OptiQuantR (with last version 0.0.1) was removed from CRAN

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

2015-08-27 0.0.1

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Package uroot updated to version 2.0-9 with previous version 2.0-6 dated 2017-01-06

Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests. P-values based on response surface regressions are available for both tests. P-values based on bootstrap are available for seasonal unit root tests. A parallel implementation of the bootstrap method requires a CUDA capable GPU with compute capability >= 3.0, otherwise a debugging version fully coded in R is used.
Author: Javier López-de-Lacalle <javlacalle@yahoo.es>
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>

Diff between uroot versions 2.0-6 dated 2017-01-06 and 2.0-9 dated 2017-01-29

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Package textTinyR updated to version 1.0.3 with previous version 1.0.2 dated 2017-01-20

Title: Text Processing for Small or Big Data Files
Description: Processes big text data files in batches efficiently. For this purpose, it offers functions for splitting, parsing, tokenizing and creating a vocabulary. Moreover, it includes functions for building either a document-term matrix or a term-document matrix and extracting information from those (term-associations, most frequent terms). Lastly, it embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between textTinyR versions 1.0.2 dated 2017-01-20 and 1.0.3 dated 2017-01-29

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Package lingtypology updated to version 1.0.1 with previous version 1.0.0 dated 2016-12-29

Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic cartography. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://agricolamz.github.io/lingtypology/> and package vignette.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>

Diff between lingtypology versions 1.0.0 dated 2016-12-29 and 1.0.1 dated 2017-01-29

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Package tmaptools updated to version 1.2 with previous version 1.0 dated 2017-01-03

Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

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Package tmap updated to version 1.8-1 with previous version 1.8 dated 2017-01-03

Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre], Joel Gombin [ctb], Sebastian Jeworutzki [ctb], Kent Russell [ctb], Richard Zijdeman [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

Diff between tmap versions 1.8 dated 2017-01-03 and 1.8-1 dated 2017-01-29

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 tmap-1.8-1/tmap/NEWS                                                             |    5 
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 tmap-1.8-1/tmap/R/process_tm.R                                                   |    6 
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 tmap-1.8-1/tmap/man/qtm.Rd                                                       |    2 
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 tmap-1.8-1/tmap/man/tm_facets.Rd                                                 |    2 
 tmap-1.8-1/tmap/man/tm_layout.Rd                                                 |    2 
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 tmap-1.8/tmap/man/polygons.Rd                                                    |only
 tmap-1.8/tmap/man/raster.Rd                                                      |only
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New package rflann with initial version 1.3
Package: rflann
Type: Package
Title: Basic R Interface to the 'FLANN' C++ Library
Version: 1.3
Date: 2017-01-28
Author: Marius Muja, David Lowe and Jeremy Yee
Maintainer: Jeremy Yee <jeremyyee@outlook.com.au>
Description: Basic R interface for the 'FLANN' C++ library version 1.8.4 written by Marius Muja and David Lowe. K-nearest neighbours searching and radius searching.
URL: https://github.com/YeeJeremy/rflann
License: GPL
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
BugReports: https://github.com/YeeJeremy/rflann/issues
Packaged: 2017-01-27 23:22:10 UTC; jeremyyee
X-CRAN-Comment: Archived on 2016-12-12 as check problems were not corrected despite reminders.
Repository: CRAN
Date/Publication: 2017-01-29 14:45:38

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New package PeerPerformance with initial version 2.1.1
Package: PeerPerformance
Version: 2.1.1
Date: 2017-01-29
Title: Luck-Corrected Peer Performance Analysis in R
Authors@R: c(person("David", "Ardia", role = c("aut", "cre"), email = "david.ardia.ch@gmail.com"), person("Kris", "Boudt", role = "aut"))
Author: David Ardia [aut, cre], Kris Boudt [aut]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Depends: snow, sandwich, lmtest, compiler
Suggests: testthat
Description: Provides functions to perform the peer performance analysis of funds' returns as described in Ardia and Boudt (2016) <doi:10.2139/ssrn.2000901>.
License: GPL (>= 2)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-01-29 12:51:31 UTC; ardiad
Repository: CRAN
Date/Publication: 2017-01-29 15:01:34

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Package bioinactivation updated to version 1.1.5 with previous version 1.1.3 dated 2016-09-18

Title: Simulation of Dynamic Microbial Inactivation
Description: Prediction and adjustment to experimental data of microbial inactivation. Several models available in the literature are implemented.
Author: Alberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>

Diff between bioinactivation versions 1.1.3 dated 2016-09-18 and 1.1.5 dated 2017-01-29

 DESCRIPTION                           |   11 
 MD5                                   |   86 +++---
 NAMESPACE                             |    2 
 NEWS.md                               |only
 build/vignette.rds                    |binary
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 inst/doc/inactivation.R               |   52 ++--
 inst/doc/inactivation.html            |  423 +++++++++++++++++-----------------
 man/Bigelow_iso.Rd                    |    2 
 man/WeibullMafart_iso.Rd              |    2 
 man/WeibullPeleg_iso.Rd               |    2 
 man/build_temperature_interpolator.Rd |    6 
 man/check_model_params.Rd             |    2 
 man/dBigelow_model.Rd                 |    4 
 man/dGeeraerd_model.Rd                |    2 
 man/dMafart_model.Rd                  |    2 
 man/dPeleg_model.Rd                   |    2 
 man/dynamic_inactivation.Rd           |    2 
 man/fit_dynamic_inactivation.Rd       |    3 
 man/fit_inactivation_MCMC.Rd          |    5 
 man/fit_isothermal_inactivation.Rd    |    9 
 man/get_isothermal_model_data.Rd      |    2 
 man/get_model_data.Rd                 |    4 
 man/get_prediction_cost.Rd            |    4 
 man/is.FitInactivation.Rd             |    2 
 man/is.FitInactivationMCMC.Rd         |    2 
 man/is.IsoFitInactivation.Rd          |    2 
 man/is.PredInactivationMCMC.Rd        |    2 
 man/is.SimulInactivation.Rd           |    2 
 man/isothermal_inactivation.Rd        |    2 
 man/laterosporus_dyna.Rd              |    2 
 man/laterosporus_iso.Rd               |    2 
 man/plot.FitInactivation.Rd           |    2 
 man/plot.FitInactivationMCMC.Rd       |    2 
 man/plot.IsoFitInactivation.Rd        |    2 
 man/plot.PredInactivationMCMC.Rd      |    2 
 man/plot.SimulInactivation.Rd         |    2 
 man/predict_inactivation.Rd           |    3 
 man/predict_inactivation_MCMC.Rd      |   24 -
 man/sample_IsoFit.Rd                  |    8 
 man/sample_MCMCfit.Rd                 |    6 
 man/sample_dynaFit.Rd                 |    6 
 man/summary.FitInactivation.Rd        |    2 
 man/summary.FitInactivationMCMC.Rd    |    2 
 man/summary.IsoFitInactivation.Rd     |    2 
 45 files changed, 365 insertions(+), 341 deletions(-)

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New package usmap with initial version 0.1.0
Package: usmap
Version: 0.1.0
Title: US Maps Including Alaska and Hawaii
Description: Obtain United States map data frames of varying region types (e.g. county, state). The map data frames include Alaska and Hawaii conveniently placed to the bottom left, as they appear in most maps of the US. Convenience functions for plotting choropleths and working with FIPS codes are also provided.
Authors@R: person("Paolo", "Di Lorenzo", email = "paolo@dilorenzo.pl", role = c("aut", "cre"))
Depends: R (>= 3.3.1)
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
URL: http://dilorenzo.pl/usmap
BugReports: http://github.com/pdil/usmap/issues
Imports: graphics, utils
Suggests: ggplot2, knitr, proto, rmarkdown, testthat
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-01-28 20:27:15 UTC; paolo
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.pl>
Repository: CRAN
Date/Publication: 2017-01-29 10:16:17

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New package tidyxl with initial version 0.2.1
Package: tidyxl
Title: Read Untidy Excel Files
Version: 0.2.1
Authors@R: c( person("Duncan", "Garmonsway", email = "nacnudus@gmail.com", role = c("aut", "cre")), person("Hadley", "Wickham", role = c("ctb"), comment = "Author of included readxl fragments"), person("RStudio", role = "cph", comment = "Copyright holder of included readxl fragments"), person("Marcin", "Kalicinski", role = c("ctb", "cph"), comment = "Author of included RapidXML code") )
Description: Imports non-tabular from Excel files into R. Exposes cell content, position and formatting in a tidy structure for further manipulation. Provides functions for selecting cells by position and relative position, and for associating data cells with header cells by proximity in given directions. Supports '.xlsx' and '.xlsm' via the embedded 'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Does not support '.xlsb' or '.xls'.
Depends: R (>= 3.2.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp
URL: https://github.com/nacnudus/tidyxl
BugReports: https://github.com/nacnudus/tidyxl/issues
RoxygenNote: 5.0.1.9000
Suggests: testthat, knitr, rmarkdown, readxl
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-01-28 19:03:27 UTC; nacnudus
Author: Duncan Garmonsway [aut, cre], Hadley Wickham [ctb] (Author of included readxl fragments), RStudio [cph] (Copyright holder of included readxl fragments), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code)
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Repository: CRAN
Date/Publication: 2017-01-29 10:16:16

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Package poio updated to version 0.0-3 with previous version 0.0-2 dated 2017-01-05

Title: Input/Output Functionality for "PO" and "POT" Message Translation Files
Description: Read and write PO and POT files, for package translations.
Author: Richard Cotton [aut, cre], Thomas Leeper [aut]
Maintainer: Richard Cotton <richierocks@gmail.com>

Diff between poio versions 0.0-2 dated 2017-01-05 and 0.0-3 dated 2017-01-29

 DESCRIPTION                      |    6 +-
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 NAMESPACE                        |    1 
 NEWS                             |    1 
 R/fix_metadata.R                 |  104 +++++++++++++++++++++++++++------------
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 README.md                        |   81 +++++++++++++++++++-----------
 man/fix_metadata.Rd              |   22 ++++++--
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 tests/testthat.R                 |   31 ++++++++++-
 tests/testthat/test-empty.R      |   68 +++++++++++++++++++++++++
 tests/testthat/test-summerof69.R |    2 
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New package MAVE with initial version 0.1.6
Package: MAVE
Type: Package
Title: Methods for Dimension Reduction
Version: 0.1.6
Date: 2017-01-16
Author: Hang Weiqiang<E0010758@u.nus.edu>,Xia Yingcun<staxyc@nus.edu.sg>
Maintainer: Hang Weiqiang<E0010758@u.nus.edu>
Description: Functions for dimension reduction, using MAVE (Minimum Average Variance Estimation), OPG (Outer Product of Gradient) and KSIR (sliced inverse regression of kernel version). Methods for selecting the best dimension are also included.
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 5.0.1
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-01-29 03:18:25 UTC; hang
Repository: CRAN
Date/Publication: 2017-01-29 10:16:10

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Package GLDreg updated to version 1.0.6 with previous version 1.0.5 dated 2016-12-26

Title: Fit GLD Regression Model and GLD Quantile Regression Model to Empirical Data
Description: Owing to the rich shapes of Generalised Lambda Distributions (GLDs), GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and Kolmogorov-Smirnov tests and data driven smooth test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su <allegro.su@gmail.com>

Diff between GLDreg versions 1.0.5 dated 2016-12-26 and 1.0.6 dated 2017-01-29

 DESCRIPTION                   |   12 ++--
 MD5                           |   16 ++---
 NAMESPACE                     |    2 
 R/GLD.lm.R                    |   62 +++++++++------------
 R/fun.simu.gld.lm.alt.R       |   31 +++++-----
 R/summaryGraphics.gld.lm.R    |  119 +++++++++++++++++++++---------------------
 man/GLD.lm.Rd                 |    2 
 man/GLDreg-package.Rd         |    8 +-
 man/summaryGraphics.gld.lm.Rd |    2 
 9 files changed, 129 insertions(+), 125 deletions(-)

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Package btergm updated to version 1.8.2 with previous version 1.8.1 dated 2016-12-06

Title: Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb], Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>

Diff between btergm versions 1.8.1 dated 2016-12-06 and 1.8.2 dated 2017-01-29

 DESCRIPTION      |    8 ++++----
 MD5              |    6 +++---
 R/btergm.R       |    6 ++++++
 R/tergmprepare.R |   32 ++++++++++++++++++++++++++------
 4 files changed, 39 insertions(+), 13 deletions(-)

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