Wed, 11 Feb 2015

Package sgof updated to version 2.2 with previous version 2.1.1 dated 2014-10-23

Title: Multiple Hypothesis Testing
Description: seven different methods for multiple testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez
Maintainer: Irene Castro Conde

Diff between sgof versions 2.1.1 dated 2014-10-23 and 2.2 dated 2015-02-11

 DESCRIPTION                  |   17 +++++++++--------
 MD5                          |   41 ++++++++++++++++++++++-------------------
 NAMESPACE                    |    2 ++
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 R/BH.R                       |    2 +-
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 23 files changed, 94 insertions(+), 60 deletions(-)

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Package RSNPset updated to version 0.4 with previous version 0.3 dated 2014-12-16

Title: Efficient Score Statistics For Genome-Wide SNP Set Analysis
Description: RSNPset is an implementation of the use of efficient score statistics in genome-wide SNP set analysis with complex traits. The package provides three standard score statistics (Cox, binomial, and Gaussian) but is easily extensible to include others. Code implementing the inferential procedure is primarily written in C++ and utilizes parallelization of the analysis to reduce runtime. A supporting function offers simple computation of observed, permutation, and FWER and FDR adjusted p-values.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley

Diff between RSNPset versions 0.3 dated 2014-12-16 and 0.4 dated 2015-02-11

 DESCRIPTION                   |   10 +-
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Package kselection updated to version 0.2.0 with previous version 0.1.1 dated 2014-10-17

Title: Selection of K in K-Means Clustering
Description: Selection of k in k-means clustering based on Pham et al. paper ``Selection of k in k-means clustering''.
Author: Daniel Rodriguez
Maintainer: Daniel Rodriguez

Diff between kselection versions 0.1.1 dated 2014-10-17 and 0.2.0 dated 2015-02-11

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New package tmg with initial version 0.3
Package: tmg
Type: Package
Title: Truncated Multivariate Gaussian Sampling
Version: 0.3
Date: 2015-02-11
Author: Ari Pakman
Maintainer: Ari Pakman
Description: Random number generation of truncated multivariate Gaussian distributions using Hamiltonian Monte Carlo. The truncation is defined using linear and/or quadratic polynomials.
License: GPL-2
Imports: Rcpp
LinkingTo: Rcpp, RcppEigen
URL: http://arxiv.org/abs/1208.4118
Packaged: 2015-02-11 18:54:14 UTC; aripakman
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-11 20:57:16

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Package shinybootstrap2 updated to version 0.2.1 with previous version 0.2 dated 2015-01-22

Title: Bootstrap 2 Web Components for Use with Shiny
Description: Provides Bootstrap 2 web components for use with the Shiny package. With versions of Shiny prior to 0.11, these Bootstrap 2 components were included as part of the package. Later versions of Shiny include Bootstrap 3, so the Bootstrap 2 components have been moved into this package for those uses who rely on features specific to Bootstrap 2.
Author: Winston Chang [aut, cre], RStudio [cph], Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library; authors listed at https://github.com/twbs/bootstrap/graphs/contributors), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Egor Khmelev [ctb, cph] (jslider library), SpryMedia Limited [ctb, cph] (DataTables library)
Maintainer: Winston Chang

Diff between shinybootstrap2 versions 0.2 dated 2015-01-22 and 0.2.1 dated 2015-02-11

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Package pez updated to version 1.0-0 with previous version 0.9-0 dated 2014-11-07

Title: Phylogenetics for the Environmental Sciences
Description: Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('shape', 'evenness', 'dispersion', and 'dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs) following ('pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares, Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse

Diff between pez versions 0.9-0 dated 2014-11-07 and 1.0-0 dated 2015-02-11

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New package rlm with initial version 1.0
Package: rlm
Type: Package
Title: Robust Fitting of Linear Model
Version: 1.0
Date: 2015-02-09
Author: Oleg Yegorov
Maintainer: Oleg Yegorov
Description: Robust fitting of linear model which can take response in matrix form.
License: GPL (>= 2)
Packaged: 2015-02-11 14:57:07 UTC; Oleg
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-11 19:58:15

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New package condMVNorm with initial version 2015.2-1
Package: condMVNorm
Title: Conditional Multivariate Normal Distribution
Version: 2015.2-1
Date: 2015-02-10
Authors@R: c(person("Ravi", "Varadhan", role = c("aut", "cre"), email = "ravi.varadhan@jhu.edu"))
Description: Computes conditional multivariate normal probabilities, random deviates and densities.
Imports: stats
Depends: R(>= 1.9.0), mvtnorm
License: GPL-2
Author: Ravi Varadhan [aut, cre]
Maintainer: Ravi Varadhan
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-02-11 17:55:04 UTC; rvaradh1
Date/Publication: 2015-02-11 19:55:24

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Package bigsplines updated to version 1.0-5 with previous version 1.0-4 dated 2014-10-03

Title: Smoothing Splines for Large Samples
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Five marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, and nominal. Parametric predictors are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig

Diff between bigsplines versions 1.0-4 dated 2014-10-03 and 1.0-5 dated 2015-02-11

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New package COMMUNAL with initial version 1.0
Package: COMMUNAL
Type: Package
Title: Robust Selection of Cluster Number K
Version: 1.0
Date: 2014-02-11
Author: Albert Chen [aut, cre], Timothy E Sweeney [aut], Olivier Gevaert [ths]
Maintainer: Albert Chen
Authors@R: c(person("Albert", "Chen", role = c("aut", "cre"), email = "acc2015@stanford.edu"), person(c("Timothy", "E"), "Sweeney", role = "aut", email = "tes17@stanford.edu"), person("Olivier", "Gevaert", role = "ths", email = "ogevaert@stanford.edu"))
Depends: R (>= 2.10), cluster
Suggests: RUnit, NMF, ConsensusClusterPlus
Imports: clValid, fpc, methods, rgl
Description: Facilitates optimal clustering of a data set. Provides a framework to run a wide range of clustering algorithms to determine the optimal number (k) of clusters in the data. Then analyzes the cluster assignments from each clustering algorithm to identify samples that repeatedly classify to the same group. We call these 'core clusters', providing a basis for later class discovery.
NeedsCompilation: no
License: GPL-2
Packaged: 2015-02-11 18:01:27 UTC; stanfordinoxford
Repository: CRAN
Date/Publication: 2015-02-11 19:55:20

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Package vcrpart updated to version 0.3-2 with previous version 0.3-1 dated 2015-01-04

Title: Tree-Based Varying Coefficient Regression for Generalized Linear and Ordinal Mixed Models
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph], Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin

Diff between vcrpart versions 0.3-1 dated 2015-01-04 and 0.3-2 dated 2015-02-11

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Package spatial updated to version 7.3-9 with previous version 7.3-8 dated 2014-03-28

Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph], Roger Bivand [ctb], William Venables [cph]
Maintainer: Brian Ripley

Diff between spatial versions 7.3-8 dated 2014-03-28 and 7.3-9 dated 2015-02-11

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New package tscount with initial version 1.0.0
Package: tscount
Type: Package
Title: Analysis of Count Time Series
Version: 1.0.0
Date: 2015-02-10
Authors@R: c( person("Tobias", "Liboschik", role=c("aut", "cre"), email="liboschik@statistik.tu-dortmund.de"), person("Roland", "Fried", role=c("aut"), email="fried@statistik.tu-dortmund.de"), person("Konstantinos", "Fokianos", role=c("aut"), email="fokianos@ucy.ac.cy"), person("Philipp", "Probst", role=c("aut"), email="philipp.probst@tu-dortmund.de"), person("Jonathan", "Rathjens", role=c("ctb"), email="jonathan.rathjens@tu-dortmund.de"))
Description: Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided. Models with the identity and with the logarithmic link function are allowed. The conditional distribution can be Poisson or Negative Binomial.
Imports: parallel, ltsa
Suggests: Matrix, xtable, gamlss.data
License: GPL-2 | GPL-3
URL: http://tscount.r-forge.r-project.org
ByteCompile: true
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2015-02-11 08:36:55 UTC; liboschik
Author: Tobias Liboschik [aut, cre], Roland Fried [aut], Konstantinos Fokianos [aut], Philipp Probst [aut], Jonathan Rathjens [ctb]
Maintainer: Tobias Liboschik
Repository: CRAN
Date/Publication: 2015-02-11 10:40:44

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Package simPH updated to version 1.3 with previous version 1.2.6.1 dated 2015-01-31

Title: Tools for Simulating and Plotting Quantities of Interest Estimated From Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud

Diff between simPH versions 1.2.6.1 dated 2015-01-31 and 1.3 dated 2015-02-11

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Package SeqFeatR updated to version 0.1.7 with previous version 0.1.5 dated 2014-06-10

Title: A Tool to Associate FASTA Sequences and Features
Description: SeqFeatR provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus

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Package rpart updated to version 4.1-9 with previous version 4.1-8 dated 2014-03-28

Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley

Diff between rpart versions 4.1-8 dated 2014-03-28 and 4.1-9 dated 2015-02-11

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Package nnet updated to version 7.3-9 with previous version 7.3-8 dated 2014-03-28

Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley

Diff between nnet versions 7.3-8 dated 2014-03-28 and 7.3-9 dated 2015-02-11

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Package KernSmooth updated to version 2.23-14 with previous version 2.23-13 dated 2014-09-14

Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut], Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley

Diff between KernSmooth versions 2.23-13 dated 2014-09-14 and 2.23-14 dated 2015-02-11

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Package DataCombine updated to version 0.2.9 with previous version 0.2.8.3 dated 2015-01-31

Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud

Diff between DataCombine versions 0.2.8.3 dated 2015-01-31 and 0.2.9 dated 2015-02-11

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Package class updated to version 7.3-12 with previous version 7.3-11 dated 2014-07-21

Title: Functions for Classification
Description: Various functions for classification.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley

Diff between class versions 7.3-11 dated 2014-07-21 and 7.3-12 dated 2015-02-11

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Package boot updated to version 1.3-15 with previous version 1.3-14 dated 2015-01-10

Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Applications" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley

Diff between boot versions 1.3-14 dated 2015-01-10 and 1.3-15 dated 2015-02-11

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Package trackObjs (with last version 1.0-18) was removed from CRAN

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

2012-09-29 1.0-18

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New package rNMF with initial version 0.5.0
Package: rNMF
Type: Package
Title: Robust Nonnegative Matrix Factorization
Description: An implementation of robust nonnegative matrix factorization (rNMF). The rNMF algorithm decomposes a nonnegative high dimension data matrix into the product of two low rank nonnegative matrices, while detecting and trimming outliers. The main function is rnmf(). The package also includes a visualization tool, see(), that arranges and prints vectorized images.
Version: 0.5.0
Author: Yifan Ethan Xu , Jiayang Sun
Maintainer: Yifan Ethan Xu
Depends: R (>= 2.14.0)
Imports: nnls, knitr
VignetteBuilder: knitr
License: GPL (>= 2)
LazyData: true
Packaged: 2015-02-11 00:55:21 UTC; yifanxu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-11 07:47:35

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New package readstata13 with initial version 0.5-3
Package: readstata13
Type: Package
Title: Import Stata 13 Data Files
Version: 0.5-3
Authors@R: c( person("Jan Marvin", "Garbuszus", email = "jan.garbuszus@ruhr-uni-bochum.de", role = c("aut")), person("Sebastian", "Jeworutzki", email="Sebastian.Jeworutzki@ruhr-uni-bochum.de", role = c("aut", "cre")), person("R Core Team", role="cph") )
Description: Function to read and write the Stata 13 file format.
URL: https://github.com/sjewo/readstata13
License: GPL-2 | file LICENSE
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp
ByteCompile: yes
Packaged: 2015-02-10 20:45:41 UTC; sj
Author: Jan Marvin Garbuszus [aut], Sebastian Jeworutzki [aut, cre], R Core Team [cph]
Maintainer: Sebastian Jeworutzki
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-11 07:50:08

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New package MazamaSpatialUtils with initial version 0.1.2
Type: Package
Package: MazamaSpatialUtils
Version: 0.1.2
Date: 2015-02-10
Title: Mazama Science Spatial Data Download and Utility Functions
Authors@R: c( person("Jonathan", "Callahan", email="jonathan.s.callahan@gmail.com", role=c("aut","cre")), person("Will", "Leahy", email="procterw@gmail.com", role=c("aut")) )
Author: Jonathan Callahan [aut, cre], Will Leahy [aut]
Maintainer: Jonathan Callahan
Depends: R (>= 3.1.0)
Imports: dplyr, rgdal, rvest, sp, stringr
Suggests: ISOcodes, knitr, lubridate, maps, testthat
Description: A suite of conversion scripts to create internally standardized spatial polygons dataframes. Utility scripts use these datasets to return values such as country, state, timezone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)
License: GPL-3
VignetteBuilder: knitr
Repository: CRAN
LazyData: true
Packaged: 2015-02-10 18:40:33 UTC; jonathancallahan
NeedsCompilation: no
Date/Publication: 2015-02-11 07:48:27

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Package gramEvol updated to version 2.0-2 with previous version 1.2-1 dated 2014-10-22

Title: Grammatical Evolution for R
Description: Context Free Grammar and Grammatical Evolution for R.
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian

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New package glmm with initial version 1.0
Package: glmm
Type: Package
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation
Version: 1.0
Date: 2015-02-10
Author: Christina Knudson
Maintainer: Christina Knudson
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
License: GPL-2
Depends: R (>= 3.1.1), trust, mvtnorm, Matrix
ByteCompile: TRUE
NeedsCompilation: yes
Packaged: 2015-02-11 02:30:53 UTC; christina
Repository: CRAN
Date/Publication: 2015-02-11 07:46:15

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Package ARPobservation updated to version 1.1 with previous version 1.0 dated 2014-05-29

Title: Tools for Simulating Direct Behavioral Observation Recording Procedures Based on Alternating Renewal Processes
Description: Tools for simulating data generated by direct observation recording. Behavior streams are simulated based on an alternating renewal process, given specified distributions of event durations and interim times. Different procedures for recording data can then be applied to the simulated behavior streams. Functions are provided for the following recording methods: continuous duration recording, event counting, momentary time sampling, partial interval recording, and whole interval recording.
Author: James E. Pustejovsky, with contributions from Daniel M. Swan
Maintainer: James E. Pustejovsky

Diff between ARPobservation versions 1.0 dated 2014-05-29 and 1.1 dated 2015-02-11

 ARPobservation-1.0/ARPobservation/vignettes/Observation-algorithms-concordance.tex |only
 ARPobservation-1.0/ARPobservation/vignettes/Observation-algorithms.tex             |only
 ARPobservation-1.1/ARPobservation/DESCRIPTION                                      |   29 
 ARPobservation-1.1/ARPobservation/MD5                                              |   69 +-
 ARPobservation-1.1/ARPobservation/NAMESPACE                                        |   13 
 ARPobservation-1.1/ARPobservation/NEWS                                             |    7 
 ARPobservation-1.1/ARPobservation/R/ARPobservation-package.r                       |    8 
 ARPobservation-1.1/ARPobservation/R/PIRapp.R                                       |only
 ARPobservation-1.1/ARPobservation/R/effect_size_estimators.R                       |only
 ARPobservation-1.1/ARPobservation/R/simulate_behavior_stream.R                     |  308 ++++++++++
 ARPobservation-1.1/ARPobservation/README.md                                        |    3 
 ARPobservation-1.1/ARPobservation/build/vignette.rds                               |binary
 ARPobservation-1.1/ARPobservation/data                                             |only
 ARPobservation-1.1/ARPobservation/demo/00Index                                     |    1 
 ARPobservation-1.1/ARPobservation/demo/study_planning.R                            |only
 ARPobservation-1.1/ARPobservation/inst/mc_est_test.R                               |only
 ARPobservation-1.1/ARPobservation/man/ARPobservation.Rd                            |    9 
 ARPobservation-1.1/ARPobservation/man/Dunlap.Rd                                    |only
 ARPobservation-1.1/ARPobservation/man/F_const.Rd                                   |    3 
 ARPobservation-1.1/ARPobservation/man/F_exp.Rd                                     |    3 
 ARPobservation-1.1/ARPobservation/man/F_gam.Rd                                     |    3 
 ARPobservation-1.1/ARPobservation/man/F_gam_mix.Rd                                 |    3 
 ARPobservation-1.1/ARPobservation/man/F_unif.Rd                                    |    3 
 ARPobservation-1.1/ARPobservation/man/F_weib.Rd                                    |    3 
 ARPobservation-1.1/ARPobservation/man/Moes.Rd                                      |only
 ARPobservation-1.1/ARPobservation/man/PIR_MOM.Rd                                   |only
 ARPobservation-1.1/ARPobservation/man/PIR_loglik.Rd                                |only
 ARPobservation-1.1/ARPobservation/man/augmented_recording.Rd                       |    3 
 ARPobservation-1.1/ARPobservation/man/continuous_duration_recording.Rd             |    3 
 ARPobservation-1.1/ARPobservation/man/eq_dist.Rd                                   |    3 
 ARPobservation-1.1/ARPobservation/man/event_counting.Rd                            |    3 
 ARPobservation-1.1/ARPobservation/man/incidence_bounds.Rd                          |only
 ARPobservation-1.1/ARPobservation/man/interim_bounds.Rd                            |only
 ARPobservation-1.1/ARPobservation/man/interval_recording.Rd                        |    3 
 ARPobservation-1.1/ARPobservation/man/logRespRatio.Rd                              |only
 ARPobservation-1.1/ARPobservation/man/momentary_time_recording.Rd                  |    3 
 ARPobservation-1.1/ARPobservation/man/prevalence_bounds.Rd                         |only
 ARPobservation-1.1/ARPobservation/man/r_MTS.Rd                                     |only
 ARPobservation-1.1/ARPobservation/man/r_PIR.Rd                                     |only
 ARPobservation-1.1/ARPobservation/man/r_WIR.Rd                                     |only
 ARPobservation-1.1/ARPobservation/man/r_behavior_stream.Rd                         |    3 
 ARPobservation-1.1/ARPobservation/man/r_continuous_recording.Rd                    |only
 ARPobservation-1.1/ARPobservation/man/r_event_counting.Rd                          |only
 ARPobservation-1.1/ARPobservation/man/reported_observations.Rd                     |    3 
 ARPobservation-1.1/ARPobservation/tests                                            |only
 45 files changed, 431 insertions(+), 58 deletions(-)

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