Fri, 24 Feb 2017

New package mixR with initial version 0.1.0
Package: mixR
Type: Package
Title: Finite Mixture Modeling for Raw and Binned Data
Version: 0.1.0
Date: 2017-02-21
Authors@R: person("Youjiao", "Yu", email = "jiaoisjiao@gmail.com", role = c("aut", "cre"))
Maintainer: Youjiao Yu <jiaoisjiao@gmail.com>
Description: Performs maximum likelihood estimation for finite mixture models for families including Normal, Weibull, Gamma and Lognormal by using EM algorithm, together with Newton-Raphson algorithm or bisection method when necessary. It also conducts mixture model selection by using information criteria or bootstrap likelihood ratio test. The data used for mixture model fitting can be raw data or binned data. The model fitting process is accelerated by using R package 'Rcpp'.
License: GPL (>= 2)
LazyData: TRUE
Imports: ggplot2 (>= 2.1.0), graphics, Rcpp (>= 0.12.8), stats
LinkingTo: Rcpp
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-02-24 20:13:42 UTC; Youjiao_Yu
Author: Youjiao Yu [aut, cre]
Repository: CRAN
Date/Publication: 2017-02-25 01:06:48

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New package betacal with initial version 0.1.0
Package: betacal
Type: Package
Title: Beta Calibration
Version: 0.1.0
Author: Telmo M Silva Filho and Meelis Kull
Maintainer: Telmo M Silva Filho <tmfilho@gmail.com>
Description: Fit beta calibration models and obtain calibrated probabilities from them.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2017-02-24 22:46:47 UTC; tmfilho
Repository: CRAN
Date/Publication: 2017-02-25 01:03:32

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Package yuimaGUI updated to version 1.0.1 with previous version 1.0.0 dated 2017-02-19

Title: A Graphical User Interface for the 'yuima' Package
Description: Provides a graphical user interface for the 'yuima' package.
Author: YUIMA Project Team
Maintainer: Emanuele Guidotti <emanuele.guidotti@studenti.unimi.it>

Diff between yuimaGUI versions 1.0.0 dated 2017-02-19 and 1.0.1 dated 2017-02-24

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Package smooth updated to version 1.7.0 with previous version 1.6.3 dated 2017-02-11

Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and in forecasting. Currently the package includes exponential smoothing models and SARIMA in state-space form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

Diff between smooth versions 1.6.3 dated 2017-02-11 and 1.7.0 dated 2017-02-24

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 67 files changed, 4098 insertions(+), 1441 deletions(-)

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Package rsparkling updated to version 0.1.1 with previous version 0.1.0 dated 2017-01-23

Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: JJ Allaire [aut], Erin LeDell [aut], Michal Malohlava [aut], Navdeep Gill [aut, cre], Jakub Hava [aut], RStudio [cph], H2O.ai [cph]
Maintainer: Navdeep Gill <navdeep@h2o.ai>

Diff between rsparkling versions 0.1.0 dated 2017-01-23 and 0.1.1 dated 2017-02-24

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Package pairwise updated to version 0.4.1 with previous version 0.3.1 dated 2015-12-03

Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation -- not estimation! -- of the Rasch item parameters for dichotomous and polytomous item responses, using a pairwise comparison approach. Person parameters (WLE) are calculated according to Warm's weighted likelihood approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>

Diff between pairwise versions 0.3.1 dated 2015-12-03 and 0.4.1 dated 2017-02-24

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Package msaR updated to version 0.2.0 with previous version 0.1.0 dated 2016-12-06

Title: Multiple Sequence Alignment for R Shiny
Description: Visualises multiple sequence alignments dynamically within the Shiny web application framework.
Author: Benedikt Rauscher [aut, cph], Zachary Charlop-Powers [cre, aut]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

Diff between msaR versions 0.1.0 dated 2016-12-06 and 0.2.0 dated 2017-02-24

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More information about msaR at CRAN
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Package lavaan updated to version 0.5-23.1097 with previous version 0.5-22 dated 2016-09-24

Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre], Daniel Oberski [ctb], Jarrett Byrnes [ctb], Leonard Vanbrabant [ctb], Victoria Savalei [ctb], Ed Merkle [ctb], Michael Hallquist [ctb], Mijke Rhemtulla [ctb], Myrsini Katsikatsou [ctb], Mariska Barendse [ctb], Michael Chow [ctb], Terrence Jorgensen [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>

Diff between lavaan versions 0.5-22 dated 2016-09-24 and 0.5-23.1097 dated 2017-02-24

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More information about lavaan at CRAN
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Package falconx updated to version 0.2 with previous version 0.1 dated 2016-04-21

Title: Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data
Description: This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data. Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual. The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.
Author: Hao Chen and Nancy R. Zhang
Maintainer: Hao Chen <hxchen@ucdavis.edu>

Diff between falconx versions 0.1 dated 2016-04-21 and 0.2 dated 2017-02-24

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More information about falconx at CRAN
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Package europop updated to version 0.3.1 with previous version 0.3 dated 2017-01-17

Title: Historical Populations of European Cities, 1500-1800
Description: This dataset contains population estimates of all European cities with at least 10,000 inhabitants during the period 1500-1800. These data are adapted from Jan De Vries, "European Urbanization, 1500-1800" (1984).
Author: Matthew Lincoln [aut, cre], Jan De Vries [aut]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>

Diff between europop versions 0.3 dated 2017-01-17 and 0.3.1 dated 2017-02-24

 DESCRIPTION          |   14 +++++++-------
 MD5                  |   14 +++++++-------
 NEWS.md              |    4 ++++
 README.md            |    3 ++-
 data/city_coords.rda |binary
 data/europop.rda     |binary
 man/city_coords.Rd   |    1 -
 man/europop.Rd       |    1 -
 8 files changed, 20 insertions(+), 17 deletions(-)

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Package ecm updated to version 0.7.0 with previous version 0.6.0 dated 2017-02-11

Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>

Diff between ecm versions 0.6.0 dated 2017-02-11 and 0.7.0 dated 2017-02-24

 DESCRIPTION    |    6 ++--
 MD5            |   12 ++++-----
 R/ecm.R        |   48 ++++++++++++++++++------------------
 R/ecmback.r    |   56 ++++++++++++++++++++++++------------------
 R/ecmpredict.r |   76 +++++++++++++++++++++++++++++++++------------------------
 man/ecm.Rd     |    3 +-
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 7 files changed, 113 insertions(+), 90 deletions(-)

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Package blavaan updated to version 0.2-3 with previous version 0.2-2 dated 2016-09-27

Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre], Yves Rosseel [aut], Mauricio Garnier-Villarreal [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>

Diff between blavaan versions 0.2-2 dated 2016-09-27 and 0.2-3 dated 2017-02-24

 blavaan-0.2-2/blavaan/man/BF.Rd               |only
 blavaan-0.2-3/blavaan/DESCRIPTION             |   17 ++-
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 blavaan-0.2-3/blavaan/R/blav_object_inspect.R |   11 ++
 blavaan-0.2-3/blavaan/R/blav_object_methods.R |   25 +----
 blavaan-0.2-3/blavaan/R/blav_utils.R          |   67 +++++++++++---
 blavaan-0.2-3/blavaan/R/blavaan.R             |  121 +++++++++++++-------------
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 blavaan-0.2-3/blavaan/R/lav_export_jags.R     |   53 ++++++++---
 blavaan-0.2-3/blavaan/R/margloglik.R          |    9 +
 blavaan-0.2-3/blavaan/R/postpred.R            |    8 +
 blavaan-0.2-3/blavaan/R/set_inits.R           |    6 -
 blavaan-0.2-3/blavaan/R/set_partable.R        |   13 ++
 blavaan-0.2-3/blavaan/R/set_priors.R          |   13 +-
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 21 files changed, 269 insertions(+), 147 deletions(-)

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Package BayesS5 updated to version 1.30 with previous version 1.22 dated 2017-01-17

Title: Bayesian Variable Selection Using Simplified Shotgun Stochastic Search with Screening (S5)
Description: In p >> n settings, full posterior sampling using existing Markov chain Monte Carlo (MCMC) algorithms is highly inefficient and often not feasible from a practical perspective. To overcome this problem, we propose a scalable stochastic search algorithm that is called the Simplified Shotgun Stochastic Search (S5) and aimed at rapidly explore interesting regions of model space and finding the maximum a posteriori(MAP) model. Also, the S5 provides an approximation of posterior probability of each model (including the marginal inclusion probabilities). This algorithm is a part of an article titled Scalable Bayesian Variable Selection Using Nonlocal Prior Densities in Ultrahigh-dimensional Settings (2017+), by Minsuk Shin, Anirban Bhattachary, and Valen E. Johnson, accepted in Statistica Sinica.
Author: Minsuk Shin and Ruoxuan Tian
Maintainer: Minsuk Shin <minsuk000@gmail.com>

Diff between BayesS5 versions 1.22 dated 2017-01-17 and 1.30 dated 2017-02-24

 DESCRIPTION           |   10 +++++-----
 MD5                   |   30 ++++++++++++++++++++----------
 NAMESPACE             |    5 +++++
 R/S5.R                |    4 ++--
 R/S5_parallel.R       |    2 +-
 R/SSS.R               |    2 +-
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 21 files changed, 59 insertions(+), 31 deletions(-)

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New package OOBCurve with initial version 0.1
Package: OOBCurve
Type: Package
Title: Out of Bag Learning Curve
Description: Provides a function to calculate the out-of-bag learning curve for random forests for any measure that is available in the 'mlr' package. Supported random forest packages are 'randomForest' and 'ranger' and trained models of these packages with the train function of 'mlr'.
Authors@R: person("Philipp", "Probst", email = "philipp_probst@gmx.de", role = c("aut", "cre"))
URL: https://github.com/PhilippPro/OOBCurve
BugReports: https://github.com/PhilippPro/OOBCurve/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.0.2), mlr (>= 2.0)
Imports: randomForest, ranger
LazyData: yes
ByteCompile: yes
Version: 0.1
Date: 2017-02-14
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2017-02-24 15:55:39 UTC; philipp
Author: Philipp Probst [aut, cre]
Maintainer: Philipp Probst <philipp_probst@gmx.de>
Repository: CRAN
Date/Publication: 2017-02-24 17:31:13

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New package ccafs with initial version 0.1.0
Package: ccafs
Type: Package
Title: Client for 'CCAFS' 'GCM' Data
Description: Client for Climate Change, Agriculture, and Food Security ('CCAFS') General Circulation Models ('GCM') data. Data is stored in Amazon 'S3', from which we provide functions to fetch data.
Version: 0.1.0
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")
License: MIT + file LICENSE
URL: https://github.com/ropensci/ccafs
BugReports: https://github.com/ropensci/ccafs/issues
Imports: rappdirs (>= 0.3.1), crul (>= 0.2.0), httr, raster (>= 2.5-8), tibble (>= 1.2), xml2 (>= 1.0.0), jsonlite (>= 1.2), data.table (>= 1.9.6)
Suggests: roxygen2 (>= 5.0.1), testthat, covr, knitr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-02-24 15:29:42 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2017-02-24 17:31:14

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Package som.nn updated to version 1.1.0 with previous version 1.0.3 dated 2017-02-09

Title: Topological k-NN Classifier Based on Self-Organising Maps
Description: A topological version of k-NN: An abstract model is build as 2-dimensional self-organising map. Samples of unknown class are predicted by mapping them on the SOM and analysing class membership of neurons in the neighbourhood.
Author: Andreas Dominik
Maintainer: Andreas Dominik <andreas.dominik@mni.thm.de>

Diff between som.nn versions 1.0.3 dated 2017-02-09 and 1.1.0 dated 2017-02-24

 DESCRIPTION                    |    6 +--
 MD5                            |   76 +++++++++++++++++++++--------------------
 NAMESPACE                      |    1 
 R/plot.SOMnn.R                 |    4 +-
 R/predict.SOMnn.R              |    8 +++-
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 R/som.nn.distance.functions.R  |    6 +--
 R/som.nn.distance.matrix.R     |    7 ++-
 R/som.nn.do.train.R            |   21 ++++++-----
 R/som.nn.export.kohonen.R      |    2 -
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 R/som.nn.run.kernel.R          |   27 ++++++++++----
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 R/som.nn.som.experimental.R    |   13 ++++---
 R/som.nn.som.gaussian.R        |only
 R/som.nn.som.internal.R        |   10 ++---
 R/som.nn.train.R               |   37 +++++++++++--------
 R/som.nn.util.R                |    6 +--
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 man/dist.fun.linear.Rd         |    2 -
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 man/norm.linear.Rd             |    2 -
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 man/predict-methods.Rd         |    8 +++-
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 man/som.nn.continue.Rd         |    4 +-
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 man/som.nn.round.votes.Rd      |    4 +-
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 man/som.nn.set.Rd              |    8 ++--
 man/som.nn.som.experimental.Rd |    6 +--
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 41 files changed, 240 insertions(+), 169 deletions(-)

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Package RVAideMemoire updated to version 0.9-63 with previous version 0.9-62 dated 2016-12-13

Title: Diverse Basic Statistical and Graphical Functions
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé <mx.herve@gmail.com>

Diff between RVAideMemoire versions 0.9-62 dated 2016-12-13 and 0.9-63 dated 2017-02-24

 DESCRIPTION                  |   11 +---
 MD5                          |   20 +++----
 NAMESPACE                    |    1 
 NEWS                         |    5 +
 R/MVA.cor.R                  |   13 +++-
 R/back.lsmeans.R             |    6 +-
 R/plotresid.R                |  116 ++++++++++++++++++++-----------------------
 R/zzz.R                      |    2 
 man/RVAideMemoire-package.Rd |    4 -
 man/back.lsmeans.Rd          |    4 -
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 11 files changed, 102 insertions(+), 92 deletions(-)

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Package profileR updated to version 0.3-4 with previous version 0.3-3 dated 2016-04-01

Title: Profile Analysis of Multivariate Data in R
Description: A suite of multivariate methods and data visualization tools to implement profile analysis and cross-validation techniques described in Davison & Davenport (2002) <DOI:10.1037/1082-989X.7.4.468>, Bulut (2013) <http://conservancy.umn.edu/handle/11299/155592>, and other published and unpublished resources. The package includes routines to perform criterion-related profile analysis, profile analysis via multidimensional scaling, moderated profile analysis, profile analysis by group, and a within-person factor model to derive score profiles.
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins <cddesjardins@gmail.com>
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>

Diff between profileR versions 0.3-3 dated 2016-04-01 and 0.3-4 dated 2017-02-24

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 profileR-0.3-4/profileR/NEWS              |    6 ++++++
 profileR-0.3-4/profileR/README.md         |   10 +++++-----
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 9 files changed, 22 insertions(+), 31 deletions(-)

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Package OpenRepGrid updated to version 0.1.10 with previous version 0.1.9 dated 2014-09-07

Title: Tools to Analyse Repertory Grid Data
Description: A set of functions to analyze repertory grid data.
Author: Mark Heckmann [aut, cre]
Maintainer: Mark Heckmann <heckmann@uni-bremen.de>

Diff between OpenRepGrid versions 0.1.9 dated 2014-09-07 and 0.1.10 dated 2017-02-24

 OpenRepGrid-0.1.10/OpenRepGrid/DESCRIPTION                                       |   24 
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 OpenRepGrid-0.1.10/OpenRepGrid/NAMESPACE                                         |   11 
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Package nlsr updated to version 2017.2.19 with previous version 2017.2.12 dated 2017-02-13

Title: Functions for Nonlinear Least Squares Solutions
Description: Provides tools for working with nonlinear least squares problems. It is intended to eventually supersede the nls() function in the R distribution. For example, nls() specifically does NOT deal with small or zero residual problems. Its Gauss-Newton method frequently stops with 'singular gradient' messages.
Author: John C Nash [aut, cre], Duncan Murdoch [aut]
Maintainer: John C Nash <nashjc@uottawa.ca>

Diff between nlsr versions 2017.2.12 dated 2017-02-13 and 2017.2.19 dated 2017-02-24

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Package mvLSW updated to version 1.1 with previous version 1.0 dated 2016-12-23

Title: Multivariate, Locally Stationary Wavelet Process Estimation
Description: Tools for analysing multivariate time series with wavelets. This includes: simulation of a multivariate locally stationary wavelet (mvLSW) process from a multivariate evolutionary wavelet spectrum (mvEWS); estimation of the mvEWS, local coherence and local partial coherence; and, estimation of the asymptotic variance for mvEWS elements. See Park, Eckley and Ombao (2014) <doi:10.1109/TSP.2014.2343937> for details.
Author: Simon Taylor [aut, cre], Tim Park [aut], Idris Eckley [ths], Rebecca Killick [ctb]
Maintainer: Simon Taylor <s.taylor2@lancaster.ac.uk>

Diff between mvLSW versions 1.0 dated 2016-12-23 and 1.1 dated 2017-02-24

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Package miscset updated to version 1.1.0 with previous version 1.0.0 dated 2016-01-25

Title: Miscellaneous Tools Set
Description: A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.
Author: Sven E. Templer
Maintainer: Sven E. Templer <sven.templer@gmail.com>

Diff between miscset versions 1.0.0 dated 2016-01-25 and 1.1.0 dated 2017-02-24

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Package gss updated to version 2.1-7 with previous version 2.1-6 dated 2016-08-28

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

Diff between gss versions 2.1-6 dated 2016-08-28 and 2.1-7 dated 2017-02-24

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 DESCRIPTION            |    8 +--
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 12 files changed, 132 insertions(+), 63 deletions(-)

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New package dynsbm with initial version 0.3
Package: dynsbm
Type: Package
Title: Dynamic Stochastic Block Models
Version: 0.3
Date: 2017-02-17
Author: Catherine Matias, Vincent Miele
Maintainer: Vincent Miele <vincent.miele@univ-lyon1.fr>
Description: Dynamic stochastic block model that combines a stochastic block model (SBM) for its static part with independent Markov chains for the evolution of the nodes groups through time, developed in Matias and Miele (2016) <doi:10.1111/rssb.12200>.
Imports: Rcpp, parallel, riverplot, RColorBrewer, grDevices, graphics, stats
LinkingTo: Rcpp
License: GPL-3
URL: http://lbbe.univ-lyon1.fr/dynsbm
NeedsCompilation: yes
Packaged: 2017-02-24 09:17:43 UTC; vmiele
Repository: CRAN
Date/Publication: 2017-02-24 16:46:52

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Package clustvarsel updated to version 2.3 with previous version 2.2 dated 2015-11-19

Title: Variable Selection for Gaussian Model-Based Clustering
Description: An R package implementing variable selection methodology for Gaussian model-based clustering which allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting MCLUST models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut], Adrian E. Raftery [aut], Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>

Diff between clustvarsel versions 2.2 dated 2015-11-19 and 2.3 dated 2017-02-24

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New package walkr with initial version 0.3.4
Package: walkr
Version: 0.3.4
Date: 2017-02-13
Type: Package
Title: Random Walks in the Intersection of Hyperplanes and the N-Simplex
Authors@R: c( person("Andy", "Yao", , "andy.yao17@gmail.com", c("aut", "cre")), person("David", "Kane", , "dave.kane@gmail.com", "aut") )
Maintainer: Andy Yao <andy.yao17@gmail.com>
Depends: R (>= 3.1), ggplot2
Suggests: testthat, knitr, grid, gridExtra
Imports: hitandrun, limSolve, MASS, Rcpp (>= 0.11.6), shinystan
Description: Consider the intersection of two spaces: the complete solution space to Ax = b and the N-simplex. The intersection of these two spaces is a non-negative convex polytope. The package walkr samples from this intersection using two Monte-Carlo Markov Chain (MCMC) methods: hit-and-run and Dikin walk. walkr also provide tools to examine sample quality.
License: GPL-3
URL: https://github.com/andyyao95/walkr
BugReports: https://github.com/andyyao95/walkr/issues
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Packaged: 2017-02-23 20:24:11 UTC; AndyYao
Author: Andy Yao [aut, cre], David Kane [aut]
X-CRAN-Comment: Archived on 2017-02-16 as check problems were not corrected despite reminders. Unarchived 2017-02-24.
Repository: CRAN
Date/Publication: 2017-02-24 08:36:02

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New package tidyRSS with initial version 1.0.0
Package: tidyRSS
Type: Package
Title: Tidy RSS for R
Version: 1.0.0
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Description: With the objective of including data from RSS feeds into your analysis, tidyRSS parses RSS and Atom xml feeds and returns a tidy data frame.
URL: https://github.com/RobertMyles/tidyrss
BugReports: https://github.com/RobertMyles/tidyrss/issues
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: true
Depends: R (>= 2.10)
Imports: dplyr (>= 0.5.0), purrr (>= 0.2.2), RCurl (>= 1.95.4.8), xml2 (>= 1.1.1), lubridate (>= 1.6.0), magrittr (>= 1.5)
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-02-23 23:21:07 UTC; robert
Repository: CRAN
Date/Publication: 2017-02-24 08:32:00

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New package TAR with initial version 1.0
Package: TAR
Type: Package
Title: Bayesian Modeling of Autoregressive Threshold Time Series Models
Version: 1.0
Date: 2017-02-19
Author: Hanwen Zhang, Fabio H. Nieto
Maintainer: Hanwen Zhang <hanwengutierrez@gmail.com>
Description: Identification and estimation of the autoregressive threshold models with Gaussian noise, as well as positive-valued time series. The package provides the identification of the number of regimes, the thresholds and the autoregressive orders, as well as the estimation of remain parameters. The package implements the methodology from the 2005 paper: Modeling Bivariate Threshold Autoregressive Processes in the Presence of Missing Data <DOI:10.1081/STA-200054435>.
Encoding: UTF-8
License: GPL (>= 2)
Depends: mvtnorm
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-02-24 02:41:45 UTC; hanwenzhang
Repository: CRAN
Date/Publication: 2017-02-24 08:31:45

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Package RSurvey updated to version 0.9.1 with previous version 0.9.0 dated 2017-02-09

Title: Geographic Information System Application
Description: A geographic information system (GIS) graphical user interface (GUI) that provides data viewing, management, and analysis tools.
Author: Jason C. Fisher [aut, cre]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>

Diff between RSurvey versions 0.9.0 dated 2017-02-09 and 0.9.1 dated 2017-02-24

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Package MMDai updated to version 1.0.1 with previous version 1.0.0 dated 2017-01-23

Title: Multivariate Multinomial Distribution Approximation and Imputation for Incomplete Data
Description: Fit incomplete categorical data with infinite mixture of multinomial distribution (Dunson and Xing (2009) <DOI:10.1198/jasa.2009.tm08439>). Perform efficient missing data imputation and other statistical inference based on joint distribution estimation.
Author: Chaojie Wang
Maintainer: Chaojie Wang <wang910930@163.com>

Diff between MMDai versions 1.0.0 dated 2017-01-23 and 1.0.1 dated 2017-02-24

 DESCRIPTION           |    6 +--
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New package liquidSVM with initial version 1.0.0
Package: liquidSVM
Type: Package
Title: A Fast and Versatile SVM Package
Version: 1.0.0
Date: 2017-02-23
Author: Ingo Steinwart, Philipp Thomann
Copyright: Ingo Steinwart <ingo.steinwart@mathematik.uni-stuttgart.de>, Philipp Thomann <philipp.thomann@mathematik.uni-stuttgart.de>, Mohammad Farooq <mohammad.farooq@mathematik.uni-stuttgart.de>
Maintainer: Philipp Thomann <philipp.thomann@mathematik.uni-stuttgart.de>
Description: Support vector machines (SVMs) and related kernel-based learning algorithms are a well-known class of machine learning algorithms, for non- parametric classification and regression. liquidSVM is an implementation of SVMs whose key features are: fully integrated hyper-parameter selection, extreme speed on both small and large data sets, inclusion of a variety of different classification and regression scenarios, and full flexibility for experts.
URL: http://www.isa.uni-stuttgart.de/software/R
License: AGPL
Depends: R (>= 2.12.0), methods
Suggests: knitr, rmarkdown, e1071, deldir, testthat
Enhances: mlr, ParamHelpers
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2017-02-23 20:12:12 UTC; thomapp
Repository: CRAN
Date/Publication: 2017-02-24 08:31:57

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New package ggraph with initial version 1.0.0
Package: ggraph
Type: Package
Title: An Implementation of Grammar of Graphics for Graphs and Networks
Version: 1.0.0
Date: 2017-02-23
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Description: The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.
License: GPL-3
LazyData: TRUE
Imports: Rcpp (>= 0.12.2), dplyr, plyr, ggforce, grid, igraph (>= 1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats, viridis
Suggests: network, knitr, rmarkdown
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Depends: R (>= 2.10), ggplot2 (>= 2.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-02-23 20:10:43 UTC; thomas
Repository: CRAN
Date/Publication: 2017-02-24 08:31:52

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Package dynr updated to version 0.1.9-20 with previous version 0.1.8-17 dated 2017-01-09

Title: Dynamic Modeling in R
Description: Dynamic modeling of all kinds in R. These include models of processes in discrete time or continuous time. They also include processes that are linear or nonlinear. Latent variables can be continuous (e.g. state space models) or discrete (e.g. regime-switching models). The general approach involves maximum likelihood estimation of single- and multi-subject models of latent time series with the extended Kalman filter and Kim filter. The user provides recipes and data which are combined into a model that is then cooked to obtain free parameter estimates.
Author: Lu Ou [aut, cre], Michael D. Hunter [aut], Sy-Miin Chow [aut]
Maintainer: Lu Ou <lzo114@psu.edu>

Diff between dynr versions 0.1.8-17 dated 2017-01-09 and 0.1.9-20 dated 2017-02-24

 dynr-0.1.8-17/dynr/man/plot-dynrCook-method.Rd    |only
 dynr-0.1.8-17/dynr/man/summary-dynrCook-method.Rd |only
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 dynr-0.1.8-17/dynr/src/MakevarsGSL.win            |only
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 dynr-0.1.9-20/dynr/DESCRIPTION                    |    8 
 dynr-0.1.9-20/dynr/MD5                            |  137 +++++++-------
 dynr-0.1.9-20/dynr/NAMESPACE                      |   30 ++-
 dynr-0.1.9-20/dynr/NEWS                           |    6 
 dynr-0.1.9-20/dynr/R/dynrCook.R                   |  185 +++++++++++++++++---
 dynr-0.1.9-20/dynr/R/dynrData.R                   |   38 +++-
 dynr-0.1.9-20/dynr/R/dynrModel.R                  |  202 +++++++++++++++++++---
 dynr-0.1.9-20/dynr/R/dynrPlot.R                   |   42 +++-
 dynr-0.1.9-20/dynr/R/dynrRecipe.R                 |  135 ++++++++++++--
 dynr-0.1.9-20/dynr/R/dynrVersion.R                |    2 
 dynr-0.1.9-20/dynr/build/partial.rdb              |binary
 dynr-0.1.9-20/dynr/cleanup                        |only
 dynr-0.1.9-20/dynr/configure.win                  |    7 
 dynr-0.1.9-20/dynr/data/EMG.txt.gz                |binary
 dynr-0.1.9-20/dynr/data/EMGsim.txt.gz             |binary
 dynr-0.1.9-20/dynr/data/NonlinearDFAsim.txt.gz    |binary
 dynr-0.1.9-20/dynr/data/PPsim.txt.gz              |binary
 dynr-0.1.9-20/dynr/data/RSPPsim.txt.gz            |binary
 dynr-0.1.9-20/dynr/data/datalist                  |   10 -
 dynr-0.1.9-20/dynr/demo/LinearSDE.R               |   14 +
 dynr-0.1.9-20/dynr/demo/NonlinearODE.R            |    6 
 dynr-0.1.9-20/dynr/demo/RSLinearDiscrete.R        |   61 +++++-
 dynr-0.1.9-20/dynr/demo/RSNonlinearODE.R          |    4 
 dynr-0.1.9-20/dynr/man/EMG.Rd                     |   58 +++---
 dynr-0.1.9-20/dynr/man/EMGsim.Rd                  |   66 +++----
 dynr-0.1.9-20/dynr/man/NonlinearDFAsim.Rd         |   70 +++----
 dynr-0.1.9-20/dynr/man/PPsim.Rd                   |   52 ++---
 dynr-0.1.9-20/dynr/man/RSPPsim.Rd                 |   58 +++---
 dynr-0.1.9-20/dynr/man/coef.dynrCook.Rd           |   65 ++++---
 dynr-0.1.9-20/dynr/man/confint.dynrCook.Rd        |only
 dynr-0.1.9-20/dynr/man/diag-character-method.Rd   |   60 +++---
 dynr-0.1.9-20/dynr/man/dynr.cook.Rd               |   77 ++++----
 dynr-0.1.9-20/dynr/man/dynr.data.Rd               |   80 ++++----
 dynr-0.1.9-20/dynr/man/dynr.ggplot.Rd             |  111 ++++++------
 dynr-0.1.9-20/dynr/man/dynr.ldl.Rd                |   38 ++--
 dynr-0.1.9-20/dynr/man/dynr.model.Rd              |   86 +++++----
 dynr-0.1.9-20/dynr/man/dynr.plotFreq.Rd           |   64 +++---
 dynr-0.1.9-20/dynr/man/dynrCook-class.Rd          |   35 ++-
 dynr-0.1.9-20/dynr/man/dynrDynamics-class.Rd      |   36 +--
 dynr-0.1.9-20/dynr/man/dynrInitial-class.Rd       |   28 +--
 dynr-0.1.9-20/dynr/man/dynrMeasurement-class.Rd   |   28 +--
 dynr-0.1.9-20/dynr/man/dynrModel-class.Rd         |   34 +--
 dynr-0.1.9-20/dynr/man/dynrNoise-class.Rd         |   28 +--
 dynr-0.1.9-20/dynr/man/dynrRecipe-class.Rd        |   48 ++---
 dynr-0.1.9-20/dynr/man/dynrRegimes-class.Rd       |   28 +--
 dynr-0.1.9-20/dynr/man/dynrTrans-class.Rd         |   28 +--
 dynr-0.1.9-20/dynr/man/internalModelPrep.Rd       |   82 ++++----
 dynr-0.1.9-20/dynr/man/logLik.dynrCook.Rd         |   65 +++----
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 dynr-0.1.9-20/dynr/man/nobs.dynrCook.Rd           |only
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 dynr-0.1.9-20/dynr/man/plot.dynrCook.Rd           |only
 dynr-0.1.9-20/dynr/man/plotFormula.Rd             |   58 +++---
 dynr-0.1.9-20/dynr/man/prep.formulaDynamics.Rd    |  110 ++++++-----
 dynr-0.1.9-20/dynr/man/prep.initial.Rd            |   68 +++----
 dynr-0.1.9-20/dynr/man/prep.loadings.Rd           |  112 ++++++------
 dynr-0.1.9-20/dynr/man/prep.matrixDynamics.Rd     |   74 ++++----
 dynr-0.1.9-20/dynr/man/prep.measurement.Rd        |  104 +++++------
 dynr-0.1.9-20/dynr/man/prep.noise.Rd              |   50 ++---
 dynr-0.1.9-20/dynr/man/prep.regimes.Rd            |   87 +++++----
 dynr-0.1.9-20/dynr/man/prep.tfun.Rd               |   68 +++----
 dynr-0.1.9-20/dynr/man/printex.Rd                 |  110 +++++------
 dynr-0.1.9-20/dynr/man/summary.dynrCook.Rd        |only
 dynr-0.1.9-20/dynr/man/vcov.dynrCook.Rd           |   40 ++--
 dynr-0.1.9-20/dynr/src/brekfis.c                  |   65 +++++--
 dynr-0.1.9-20/dynr/src/glue.c                     |    1 
 dynr-0.1.9-20/dynr/src/mainR.c                    |   20 +-
 dynr-0.1.9-20/dynr/src/math_function.c            |   61 ++++++
 dynr-0.1.9-20/dynr/src/math_function.h            |   10 +
 dynr-0.1.9-20/dynr/tools/prep                     |    2 
 76 files changed, 1979 insertions(+), 1273 deletions(-)

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Package DDD updated to version 3.4 with previous version 3.3 dated 2016-11-07

Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>. Also contains functions to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

Diff between DDD versions 3.3 dated 2016-11-07 and 3.4 dated 2017-02-24

 DESCRIPTION            |    8 ++++----
 MD5                    |   25 +++++++++++++------------
 R/dd_KI_loglik.R       |    8 +++-----
 R/dd_SR_ML.R           |    2 +-
 R/dd_SR_sim.R          |    4 ++--
 R/dd_logliknorm_rhs3.R |    2 +-
 R/dd_sim.R             |    3 ++-
 R/dd_utils.R           |   49 +++++++++++++++++++++++++++++++++++++++++++++++++
 man/DDD-package.Rd     |   10 +++++++---
 man/L2brts.Rd          |only
 man/dd_LR.Rd           |    3 ---
 man/dd_ML.Rd           |    3 ---
 man/dd_SR_sim.Rd       |    6 +++---
 man/dd_sim.Rd          |    6 +++---
 14 files changed, 88 insertions(+), 41 deletions(-)

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New package autothresholdr with initial version 0.2.0
Package: autothresholdr
Type: Package
Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Version: 0.2.0
Authors@R: c( person("Rory", "Nolan", email = "rorynoolan@gmail.com", role = c("aut", "cre")), person("Gabriel", "Landini", email = "G.Landini@bham.ac.uk", role = "ctb"))
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Description: Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <http://imagej.net/Auto_Threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.
License: GPL-3
LazyData: TRUE
Imports: rJava, RSAGA, magrittr, EBImage
SystemRequirements: Java
RoxygenNote: 6.0.1
URL: https://www.github.com/rorynolan/autothresholdr
BugReports: https://www.github.com/rorynolan/autothresholdr/issues
Suggests: testthat, covr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-02-23 18:17:54 UTC; rnolan
Author: Rory Nolan [aut, cre], Gabriel Landini [ctb]
Repository: CRAN
Date/Publication: 2017-02-24 08:31:47

More information about autothresholdr at CRAN
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Package GeneticTools (with last version 0.3.1) was removed from CRAN

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

2015-02-04 0.3.1
2014-08-06 0.3
2013-10-14 0.2.1
2013-03-17 0.2
2012-12-27 0.1

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