Sun, 04 Sep 2016

Package stpm updated to version 1.3.4 with previous version 1.3.2 dated 2016-07-01

Title: Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided. For more information, see: (i) "Life tables with covariates: Dynamic model for nonlinear analysis of longitudinal data" by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80), <DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al. (2007), Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>; (iii) "Health decline, aging and mortality: how are they related?" by Yashin A. et al. (2007), Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>

Diff between stpm versions 1.3.2 dated 2016-07-01 and 1.3.4 dated 2016-09-04

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Package spaMM updated to version 1.10.0 with previous version 1.9.16 dated 2016-07-21

Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: Fran├žois Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [ctb], Dirk Eddelbuettel [ctb] (ziggurat rnorm sources), GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: Fran├žois Rousset <francois.rousset@umontpellier.fr>

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Package derivmkts updated to version 0.2.2 with previous version 0.2.1 dated 2016-06-27

Title: Functions and R Code to Accompany Derivatives Markets
Description: A set of pricing and expository functions that should be useful in teaching a course on financial derivatives.
Author: Robert McDonald [aut, cre, cph]
Maintainer: Robert McDonald <rmcd1024@gmail.com>

Diff between derivmkts versions 0.2.1 dated 2016-06-27 and 0.2.2 dated 2016-09-04

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Package Rcpp updated to version 0.12.7 with previous version 0.12.6 dated 2016-07-19

Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between Rcpp versions 0.12.6 dated 2016-07-19 and 0.12.7 dated 2016-09-04

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Package nplr updated to version 0.1-5 with previous version 0.1-4 dated 2015-08-01

Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. Can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre], Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>

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New package rcompanion with initial version 0.5.0
Package: rcompanion
Version: 0.5.0
Date: 2016-09-01
Title: Functions and Datasets for rcompanion.org
Authors@R: person("Salvatore","Mangiafico",email="mangiafico@njaes.rutgers.edu",role=c("aut","cre"))
Description: Functions and datasets to support "Summary and Analysis of Extension Education Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at http://rcompanion.org.
URL: http://rcompanion.org/
Depends: R (>= 3.3.1)
Imports: stats (>= 3.3.1), graphics (>= 3.3.1), boot (>= 1.3-18), DescTools (>= 0.99.17), multcompView (>= 0.1-7), plyr (>= 1.8.4), EMT (>= 1.1), coin (>= 1.1-2), lattice (>= 0.20-33), RVAideMemoire (>= 0.9-60), nortest (>= 1.0-4), hermite (>= 1.1.1)
Suggests:
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-09-04 17:21:23 UTC; salma
Repository: CRAN
Date/Publication: 2016-09-04 20:48:16

More information about rcompanion at CRAN
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Package googleAuthR updated to version 0.4.0 with previous version 0.3.1 dated 2016-06-25

Title: Easy Authentication with Google OAuth2 API
Description: Create R functions that interact with OAuth2 Google APIs easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre], Jennifer Bryan [ctb], Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

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New package fontquiver with initial version 0.1.0
Package: fontquiver
Title: Set of Installed Fonts
Version: 0.1.0
Authors@R: person("Lionel", "Henry", , "lionel.hry@gmail.com", c("cre", "aut"))
Description: Provides a set of fonts with permissive licences. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.
Depends: R (>= 3.3.0)
Imports: fontBitstreamVera (>= 0.1.0)
Suggests: testthat, htmltools
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-09-04 09:57:06 UTC; lionel
Author: Lionel Henry [cre, aut]
Maintainer: Lionel Henry <lionel.hry@gmail.com>
Repository: CRAN
Date/Publication: 2016-09-04 20:14:36

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New package DMRMark with initial version 1.0
Package: DMRMark
Type: Package
Title: DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data
Version: 1.0
Date: 2016-09-04
Author: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Depends: MCMCpack, mvtnorm, ellipse
Maintainer: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Description: Perform differential analysis for methylation array data. Detect differentially methylated regions (DMRs) from array M-values. The core is a Non-homogeneous Hidden Markov Model for estimating spatial correlation and a novel Constrained Gaussian Mixture Model for modeling the M-value pairs of each individual locus.
License: GPL
Packaged: 2016-09-04 08:09:56 UTC; Office
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-09-04 20:14:25

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Package distrMod updated to version 2.6.1 with previous version 2.5.3 dated 2014-11-25

Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and 'distrEx'.
Author: Matthias Kohl [aut, cph], Peter Ruckdeschel [cre, cph], R Core Team [ctb, cph] (for source file 'format.perc')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>

Diff between distrMod versions 2.5.3 dated 2014-11-25 and 2.6.1 dated 2016-09-04

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 86 files changed, 4210 insertions(+), 3528 deletions(-)

More information about distrMod at CRAN
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Package distrEllipse updated to version 2.6.2 with previous version 2.5 dated 2013-09-13

Title: S4 Classes for Elliptically Contoured Distributions
Description: Distribution (S4-)classes for elliptically contoured distributions (based on package 'distr').
Author: Peter Ruckdeschel [cre, aut, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>

Diff between distrEllipse versions 2.5 dated 2013-09-13 and 2.6.2 dated 2016-09-04

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 R/MVNorm.R                              |    4 -
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 inst/NEWS                               |   19 +++++++++
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 31 files changed, 250 insertions(+), 127 deletions(-)

More information about distrEllipse at CRAN
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Package quantreg updated to version 5.29 with previous version 5.26 dated 2016-06-13

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

Diff between quantreg versions 5.26 dated 2016-06-13 and 5.29 dated 2016-09-04

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 quantreg/src/rq0.f                                                    |    2 
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Package mixOmics updated to version 6.1.0 with previous version 6.0.0 dated 2016-06-14

Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>

Diff between mixOmics versions 6.0.0 dated 2016-06-14 and 6.1.0 dated 2016-09-04

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 mixOmics-6.1.0/mixOmics/man/vip.Rd                      |    2 
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 107 files changed, 2088 insertions(+), 1242 deletions(-)

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Package evclust updated to version 1.0.3 with previous version 1.0.2 dated 2016-05-29

Title: Evidential Clustering
Description: Various clustering algorithms that produce a credal partition, i.e., a set of Dempster-Shafer mass functions representing the membership of objects to clusters. The mass functions quantify the cluster-membership uncertainty of the objects. The algorithms are: Evidential c-Means (ECM), Relational Evidential c-Means (RECM), Constrained Evidential c-Means (CECM), EVCLUS and EK-NNclus.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>

Diff between evclust versions 1.0.2 dated 2016-05-29 and 1.0.3 dated 2016-09-04

 DESCRIPTION                |    8 +--
 MD5                        |   49 ++++++++++++-----------
 NAMESPACE                  |    2 
 R/cecm.R                   |   16 ++++---
 R/createD.R                |    2 
 R/createPairs.R            |    2 
 R/ecm.R                    |    2 
 R/evclust.R                |    3 -
 R/kevclus.R                |   83 +++++++++++++++++++++++++++++-----------
 R/plaus_dist.R             |only
 R/plot.credpart.R          |    9 +---
 R/recm.R                   |    2 
 build/vignette.rds         |binary
 inst/doc/Introduction.R    |    6 +-
 inst/doc/Introduction.Rmd  |   12 ++---
 inst/doc/Introduction.html |   92 ++++++++++++++++++++++-----------------------
 man/cecm.Rd                |    8 +--
 man/createD.Rd             |    2 
 man/createPairs.Rd         |    2 
 man/ecm.Rd                 |    2 
 man/evclust.Rd             |    3 -
 man/kevclus.Rd             |   16 ++++---
 man/plot.credpart.Rd       |    7 +--
 man/recm.Rd                |    2 
 vignettes/Introduction.Rmd |   12 ++---
 vignettes/tdenoeux.bib     |    7 +--
 26 files changed, 196 insertions(+), 153 deletions(-)

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New package advclust with initial version 0.4
Package: advclust
Type: Package
Title: Object Oriented Advanced Clustering
Version: 0.4
Date: 2016-09-03
Author: Achmad Fauzi Bagus F, Setia Pramana
Maintainer: Achmad Fauzi Bagus F <fauzi.pandya@gmail.com>
Description: S4 Object Oriented for Advanced Fuzzy Clustering and Fuzzy COnsensus Clustering. Techniques that provided by this package are Fuzzy C-Means, Gustafson Kessel (Babuska Version), Gath-Geva, Sum Voting Consensus, Product Voting Consensus, and Borda Voting Consensus. This package also provide visualization via Biplot and Radar Plot.
License: GPL-2
Depends: R (>= 3.2.5)
Imports: knitr, methods, MASS, clue, ggplot2, reshape2
LazyData: TRUE
RoxygenNote: 5.0.1
Collate: 'as_Membership.R' 'biplot.R' 'c_fuzzycluster.R' 'class_membership.R' 'class_co_fuzzycluster.R' 'class_fuzzycluster.R' 'class_fuzzycluster_list.R' 'class_validation.R' 'co.vote.R' 'cpair_fuzzy.R' 'fuzzy.CM.R' 'fuzzy.GG.R' 'fuzzy.GK.R' 'is_Membership.R' 'membership.R' 'method_co_fuzzycluster.R' 'method_fuzzycluster.R' 'method_fuzzycluster_list.R' 'method_membership.R' 'method_validation.R' 'minWeightBipartiteMatching.R' 'print_Membership.R' 'print_co_fuzzycluster.R' 'print_fuzzycluster.R' 'print_validation.R' 'radarplot.R' 'validation.R' 'zzz.R'
Suggests: rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-09-04 07:44:51 UTC; Achmad Fauzi
Repository: CRAN
Date/Publication: 2016-09-04 13:48:57

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New package RcmdrPlugin.FuzzyClust with initial version 1.1
Package: RcmdrPlugin.FuzzyClust
Type: Package
Title: R Commander Plug-in for Fuzzy Clustering Methods (Fuzzy C-Means and Gustafson Kessel)
Version: 1.1
Date: 2016-09-03
Author: Achmad Fauzi Bagus F <uzi.fauz@gmail.com>, Setia Pramana
Maintainer: Achmad Fauzi Bagus F <uzi.fauz@gmail.com>
Description: The R Commander Plug-in for Fuzzy Clustering Methods. This Plug- in provide Graphical User Interface of 2 methods of Fuzzy Clustering (Fuzzy C- Means /FCM and Gustafson Kessel-Babuska). For validation of clustering, this plug- in use Xie Beni Index, MPC index, and CE index. For statistical test (test of significant differences of grouping/clustering), this plug-in use MANOVA analysis with Pillai trace statistics. For stabilize the result, this package provide soft voting cluster ensemble function. Visualization of result are provided via plugin that must be load in Rcmdr file.
Depends: R (>= 3.2.5)
Imports: Rcmdr, doParallel, tcltk2, foreach, clue, ggplot2, MASS, reshape2, tkrplot, iterators, parallel
Suggests: knitr, rmarkdown
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-09-03 21:57:09 UTC; Achmad Fauzi
Repository: CRAN
Date/Publication: 2016-09-04 09:36:21

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New package fontBitstreamVera with initial version 0.1.0
Package: fontBitstreamVera
Title: Fonts with Bitstream Vera Fonts Licence
Version: 0.1.0
Authors@R: c( person("Lionel", "Henry", , "lionel.hry@gmail.com", c("cre", "aut")), person("Bitstream", role = "cph"))
Description: Provides fonts licenced under the Bitstream Vera Fonts licence for the fontquiver package.
Depends: R (>= 3.3.0)
License: file LICENCE
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-09-03 19:36:18 UTC; lionel
Author: Lionel Henry [cre, aut], Bitstream [cph]
Maintainer: Lionel Henry <lionel.hry@gmail.com>
License_is_FOSS: yes
Repository: CRAN
Date/Publication: 2016-09-04 10:01:34

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Package dtwclust updated to version 2.2.1 with previous version 2.2.0 dated 2016-09-02

Title: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Description: Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>

Diff between dtwclust versions 2.2.0 dated 2016-09-02 and 2.2.1 dated 2016-09-04

 DESCRIPTION                        |    8 ++++----
 MD5                                |   14 +++++++-------
 inst/NEWS.Rd                       |    2 +-
 inst/doc/dtwclust.R                |   18 +++++++++---------
 inst/doc/dtwclust.Rnw              |   22 +++++++++++-----------
 inst/doc/dtwclust.pdf              |binary
 vignettes/dtwclust-concordance.tex |    4 ++--
 vignettes/dtwclust.Rnw             |   22 +++++++++++-----------
 8 files changed, 45 insertions(+), 45 deletions(-)

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Package bootnet updated to version 0.3 with previous version 0.2 dated 2016-01-19

Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures and centrality indices. Allows for flexible specification of any undirected network estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler', 'glasso', 'huge' and 'parcor' packages.
Author: Sacha Epskamp and Eiko I. Fried
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

Diff between bootnet versions 0.2 dated 2016-01-19 and 0.3 dated 2016-09-04

 bootnet-0.2/bootnet/R/bootstrapIncreasesEdges.R |only
 bootnet-0.2/bootnet/R/evenMoreTests.R           |only
 bootnet-0.3/bootnet/DESCRIPTION                 |   16 
 bootnet-0.3/bootnet/MD5                         |   32 -
 bootnet-0.3/bootnet/NAMESPACE                   |   11 
 bootnet-0.3/bootnet/NEWS                        |only
 bootnet-0.3/bootnet/R/Smetric.R                 |only
 bootnet-0.3/bootnet/R/bootTable.R               |   78 ++-
 bootnet-0.3/bootnet/R/bootnet.R                 |  623 +++++++++++++-----------
 bootnet-0.3/bootnet/R/bootnetResultsMethods.R   |    6 
 bootnet-0.3/bootnet/R/centralityCompare.R       |only
 bootnet-0.3/bootnet/R/checkDefault.R            |only
 bootnet-0.3/bootnet/R/checkInput.R              |only
 bootnet-0.3/bootnet/R/estimateNetwork.R         |  105 +++-
 bootnet-0.3/bootnet/R/plotMethod.R              |  537 +++++++++++++++-----
 bootnet-0.3/bootnet/R/printMethod.R             |   50 +
 bootnet-0.3/bootnet/R/zzz.R                     |only
 bootnet-0.3/bootnet/inst                        |only
 bootnet-0.3/bootnet/man/bootnet.Rd              |  177 ++----
 bootnet-0.3/bootnet/man/corStability.Rd         |only
 bootnet-0.3/bootnet/man/differenceTest.Rd       |only
 bootnet-0.3/bootnet/man/estimateNetwork.Rd      |only
 bootnet-0.3/bootnet/man/plot.bootnet.Rd         |   16 
 23 files changed, 1075 insertions(+), 576 deletions(-)

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