Mon, 30 May 2016

Package iemiscdata updated to version 0.5.1 with previous version 0.5.0 dated 2016-02-04

Title: Irucka Embry's Miscellaneous Data Collection
Description: Miscellaneous data sets [Environmental/Water Resources Engineering].
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between iemiscdata versions 0.5.0 dated 2016-02-04 and 0.5.1 dated 2016-05-30

 DESCRIPTION |   14 ++++++++------
 MD5         |   11 +++++++++--
 NEWS.md     |    7 +++++++
 build       |only
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 vignettes   |only
 6 files changed, 24 insertions(+), 8 deletions(-)

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Package iemisc updated to version 0.6.2 with previous version 0.5.1 dated 2016-05-18

Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions (Engineering Economics, Environmental/Water Resources Engineering, Geometry, Statistics, GNU Octave length functions, etc.).
Author: Irucka Embry [aut, cre]. Includes R source code and/or documentation previously published by: Felix Andrews (zoo) and Hans Werner Borchers (pracma). [Borrowed from DescTools description.]
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between iemisc versions 0.5.1 dated 2016-05-18 and 0.6.2 dated 2016-05-30

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 NAMESPACE          |    1 
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Package CRF updated to version 0.3-9 with previous version 0.3-8 dated 2014-07-30

Title: Conditional Random Fields
Description: Implements modeling and computational tools for conditional random fields (CRF) model as well as other probabilistic undirected graphical models of discrete data with pairwise and unary potentials.
Author: Ling-Yun Wu [aut, cre]
Maintainer: Ling-Yun Wu <wulingyun@gmail.com>

Diff between CRF versions 0.3-8 dated 2014-07-30 and 0.3-9 dated 2016-05-30

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Package qwraps2 updated to version 0.2.1 with previous version 0.2.0 dated 2016-04-24

Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into '.Rnw' or '.Rmd' files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at <https://github.com/dewittpe/qwraps/>. The implementation and limited scope of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre], Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>

Diff between qwraps2 versions 0.2.0 dated 2016-04-24 and 0.2.1 dated 2016-05-30

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Package QICD updated to version 1.1.1 with previous version 1.0.1 dated 2016-02-29

Title: Estimate the Coefficients for Non-Convex Penalized Quantile Regression Model by using QICD Algorithm
Description: Extremely fast algorithm "QICD", Iterative Coordinate Descent Algorithm for High-dimensional Nonconvex Penalized Quantile Regression. This algorithm combines the coordinate descent algorithm in the inner iteration with the majorization minimization step in the outside step. For each inner univariate minimization problem, we only need to compute a one-dimensional weighted median, which ensures fast computation. Tuning parameter selection is based on two different method: the cross validation and BIC for quantile regression model. Details are described in the Peng,B and Wang,L. (2015) linked to via the URL below with <DOI:10.1080/10618600.2014.913516>.
Author: Bo Peng [aut, cre], Rondall E. Jones [ctb], John A. Wisniewski [ctb]
Maintainer: Bo Peng <peng0199@umn.edu>

Diff between QICD versions 1.0.1 dated 2016-02-29 and 1.1.1 dated 2016-05-30

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Sun, 29 May 2016

Package qrmtools updated to version 0.0-6 with previous version 0.0-5 dated 2016-02-13

Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from the book "Quantitative Risk Management: Concepts, Techniques and Tools". Furthermore, new developments and auxiliary functions for Quantitative Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

Diff between qrmtools versions 0.0-5 dated 2016-02-13 and 0.0-6 dated 2016-05-29

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New package rcss with initial version 1.0
Package: rcss
Type: Package
Title: Convex Switching Systems
Version: 1.0
Date: 2016-05-26
Author: Juri Hinz and Jeremy Yee
Maintainer: Jeremy Yee <jeremyyee@outlook.com.au>
Description: The numerical treatment of optimal switching problems in a finite time setting when the state evolves as a controlled Markov chain consisting of a uncontrolled continuous component following linear dynamics and a controlled Markov chain taking values in a finite set. The reward functions are assumed to be convex and Lipschitz continuous in the continuous state. The action set is finite.
License: GPL
Depends: rflann (>= 1.0)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp, RcppArmadillo
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: yes
Packaged: 2016-05-29 15:41:10 UTC; jeremyyee
Repository: CRAN
Date/Publication: 2016-05-29 21:14:04

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Package pracma updated to version 1.9.3 with previous version 1.8.8 dated 2015-11-27

Title: Practical Numerical Math Functions
Description: Functions from numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

Diff between pracma versions 1.8.8 dated 2015-11-27 and 1.9.3 dated 2016-05-29

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Package BOIN updated to version 2.3 with previous version 2.2 dated 2016-04-22

Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials. The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>

Diff between BOIN versions 2.2 dated 2016-04-22 and 2.3 dated 2016-05-29

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Package adagio updated to version 0.6.5 with previous version 0.6.3 dated 2015-12-06

Title: Discrete and Global Optimization Routines
Description: The R package 'adagio' will provide methods and algorithms for discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

Diff between adagio versions 0.6.3 dated 2015-12-06 and 0.6.5 dated 2016-05-29

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New package waterfalls with initial version 0.1.0
Package: waterfalls
Type: Package
Title: Create Waterfall Charts
Version: 0.1.0
Author: Hugh Parsonage
Maintainer: Hugh Parsonage <hugh.parsonage+waterfall@gmail.com>
Description: There seems to be no simple way to create 'waterfall charts' in 'ggplot2' currently. This package contains a single function (waterfall) that draws simply a waterfall chart as a 'ggplot2' object. Some flexibility in the appearance is available.
License: MIT + file LICENSE
Imports: ggplot2 (>= 2.0.0),
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-29 07:45:35 UTC; hughGrattan
Repository: CRAN
Date/Publication: 2016-05-29 15:21:34

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New package rflann with initial version 1.0
Package: rflann
Type: Package
Title: Basic R Interface to the FLANN C++ Library
Version: 1.0
Date: 2016-05-28
Author: Marius Muja, David Lowe and Jeremy Yee
Maintainer: Jeremy Yee <jeremyyee@outlook.com.au>
Description: Basic R interface for the FLANN C++ library written by Marius Muja and David Lowe. This package was written primarily for another package, 'rcss'. This packages utilises a few features from the FLANN C++ library. When I have time (and if there is sufficient demand), I will add more functions.
License: GPL
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2016-05-29 07:41:50 UTC; jeremyyee
Repository: CRAN
Date/Publication: 2016-05-29 15:20:18

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New package qrmdata with initial version 2016-01-03-1
Package: qrmdata
Version: 2016-01-03-1
Encoding: UTF-8
Title: Data Sets for Quantitative Risk Management Practice
Description: Various data sets (stocks, stock indices, constituent data, FX, zero-coupon bond yield curves, volatility, commodities) for Quantitative Risk Management practice.
Authors@R: c(person(given = "Marius", family = "Hofert", role = c("aut", "cre"), email = "marius.hofert@uwaterloo.ca"), person(given = "Kurt", family = "Hornik", role = "aut", email = "Kurt.Hornik@R-project.org"))
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Depends: R (>= 3.0.0)
Imports: xts
Suggests: knitr, qrmtools
Enhances:
License: GPL-2 | GPL-3
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-05-29 16:54:37
Packaged: 2016-05-29 12:56:37 UTC; mhofert

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Package NNS updated to version 0.1.9 with previous version 0.1.6 dated 2016-05-11

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>

Diff between NNS versions 0.1.6 dated 2016-05-11 and 0.1.9 dated 2016-05-29

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Package rbamtools updated to version 2.16.0 with previous version 2.14.3 dated 2016-02-07

Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

Diff between rbamtools versions 2.14.3 dated 2016-02-07 and 2.16.0 dated 2016-05-29

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Package quint updated to version 1.2.0 with previous version 1.0 dated 2013-11-08

Title: Qualitative Interaction Trees
Description: Grows a qualitative interaction tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm randomized controlled trial.
Author: Elise Dusseldorp [aut, cre, cph], Lisa Doove [aut], Jeanne van de Put [aut], Cor Ninaber [ctb] (supported with the plot function), Iven Van Mechelen [aut, cph]
Maintainer: Elise Dusseldorp <elise.dusseldorp@fsw.leidenuniv.nl>

Diff between quint versions 1.0 dated 2013-11-08 and 1.2.0 dated 2016-05-29

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Permanent link

Package MetaLandSim updated to version 0.5.2 with previous version 0.5.1 dated 2016-05-05

Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>

Diff between MetaLandSim versions 0.5.1 dated 2016-05-05 and 0.5.2 dated 2016-05-29

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Package evclust updated to version 1.0.2 with previous version 1.0.1 dated 2016-05-28

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>

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Sat, 28 May 2016

New package cocor with initial version 1.1-3
Package: cocor
Type: Package
Title: Comparing Correlations
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen <mail@birkdiedenhofen.de>
Depends: methods
Suggests: testthat
Enhances: rkward
Imports: stats
Description: Statistical tests for the comparison between two correlations based on either independent or dependent groups. Dependent correlations can either be overlapping or nonoverlapping. A web interface is available on the website http://comparingcorrelations.org. A plugin for the R GUI and IDE RKWard is included. Please install RKWard from https://rkward.kde.org to use this feature. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
URL: http://comparingcorrelations.org
Authors@R: c(person(given="Birk", family="Diedenhofen", email="mail@birkdiedenhofen.de", role=c("aut", "cre")))
Version: 1.1-3
Date: 2016-05-28
RoxygenNote: 5.0.1
Collate: '0helper.r' 'as.htest.r' 'cocor-package.R' 'cocor.dep.groups.nonoverlap.r' 'cocor.dep.groups.overlap.r' 'cocor.indep.groups.r' 'cocor.r' 'get.cocor.input.r' 'get.cocor.results.r'
NeedsCompilation: no
Packaged: 2016-05-28 16:24:29 UTC; birk
Repository: CRAN
Date/Publication: 2016-05-28 20:30:27

More information about cocor at CRAN
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Package CHNOSZ updated to version 1.0.8 with previous version 1.0.7 dated 2015-11-19

Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry and low-temperature geochemistry. The features include calculation of the standard molal thermodynamic properties and chemical affinities of reactions involving minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous species; amino acid group additivity for the standard molal thermodynamic properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state for aqueous species; construction of equilibrium activity diagrams as a function of temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>

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Package varbvs updated to version 2.0.0 with previous version 1.0 dated 2012-04-10

Title: Large-Scale Bayesian Variable Selection Using Variational Methods
Description: Fast algorithms for fitting Bayesian variable selection models and computing Bayes factors, in which the outcome (or response variable) is modeled using a linear regression or a logistic regression. The algorithms are based on the variational approximations described in "Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies" (P. Carbonetto & M. Stephens, 2012, <DOI:10.1214/12-BA703>). This software has been applied to large data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto, Matthew Stephens
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>

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New package riem with initial version 0.1.0
Package: riem
Type: Package
Title: Accesses Weather Data from the Iowa Environment Mesonet
Version: 0.1.0
Authors@R: c(person("Maëlle", "Salmon", email = "maelle.salmon@yahoo.se", role = c("aut", "cre")), person("Brooke", "Anderson", role = c("rev"), comment = "Brooke Anderson reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/39."))
Description: Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.
License: GPL (>= 2)
LazyData: TRUE
Imports: httr (>= 1.1.0), lubridate (>= 1.5.6), dplyr (>= 0.4.3), jsonlite (>= 0.9.19), readr (>= 0.2.2), lazyeval (>= 0.1.10)
RoxygenNote: 5.0.1
URL: http://github.com/ropenscilabs/riem
BugReports: http://github.com/ropenscilabs/riem/issues
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-05-28 13:36:04 UTC; Maelle
Author: Maëlle Salmon [aut, cre], Brooke Anderson [rev] (Brooke Anderson reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/39.)
Maintainer: Maëlle Salmon <maelle.salmon@yahoo.se>
Repository: CRAN
Date/Publication: 2016-05-28 15:52:50

More information about riem at CRAN
Permanent link

Package itsadug updated to version 2.1 with previous version 2.0 dated 2016-03-20

Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).
Author: Jacolien van Rij [aut, cre], Martijn Wieling [aut], R. Harald Baayen [aut], Hedderik van Rijn [ctb]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>

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Package htmltab updated to version 0.7.0 with previous version 0.6.0 dated 2015-07-22

Title: Assemble Data Frames from HTML Tables
Description: HTML tables are a valuable data source but extracting and recasting these data into a useful format can be tedious. This package allows to collect structured information from HTML tables. It is similar to readHTMLTable() of the XML package but provides three major advantages. First, the function automatically expands row and column spans in the header and body cells. Second, users are given more control over the identification of header and body rows which will end up in the R table, including semantic header information that appear throughout the body. Third, the function preprocesses table code, corrects common types of malformations, removes unneeded parts and so helps to alleviate the need for tedious post-processing.
Author: Christian Rubba [aut, cre]
Maintainer: Christian Rubba <christian.rubba@gmail.com>

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 htmltab-0.7.0/htmltab/tests/testthat/test_expand_spans.R |    1 
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 htmltab-0.7.0/htmltab/vignettes/htmltab.Rmd              |   15 -
 39 files changed, 369 insertions(+), 227 deletions(-)

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Permanent link

New package ZeligEI with initial version 0.1-0
Package: ZeligEI
Maintainer: James Honaker <zelig.zee@gmail.com>
License: GPL (>= 2)
Title: Zelig Ecological Inference Models
Author: James Honaker
Description: Add-on package for Zelig 5. Enables the use of a variety of ecological inference models.
Version: 0.1-0
Date: 2016-05-27
Imports: methods, Zelig (>= 5.0-11), MASS, jsonlite, dplyr, eiPack, ei, MCMCpack
Suggests: testthat, knitr
Collate: 'create-json.R' 'model-ei.R' 'model-dynamic-ei.R' 'model-hier-ei.R' 'model-ml-ei.R' 'model-rxc-ei.R'
NeedsCompilation: no
Packaged: 2016-05-28 03:41:40 UTC; tercer
Repository: CRAN
Date/Publication: 2016-05-28 08:18:30

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Package rdrobust updated to version 0.91 with previous version 0.90 dated 2016-05-08

Title: Robust Data-Driven Statistical Inference in Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell, <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>

Diff between rdrobust versions 0.90 dated 2016-05-08 and 0.91 dated 2016-05-28

 DESCRIPTION    |    8 ++++----
 MD5            |    8 ++++----
 R/functions.R  |    2 +-
 R/rdbwselect.R |   12 ++++++------
 R/rdrobust.R   |   12 ++++++------
 5 files changed, 21 insertions(+), 21 deletions(-)

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New package preprosim with initial version 0.1.0
Package: preprosim
Type: Package
Title: Lightweight Data Quality Simulation for Classification
Version: 0.1.0
Date: 2016-05-28
Authors@R: person("Markus", "Vattulainen", email = "markus.vattulainen@gmail.com", role = c("aut", "cre"))
Description: Data quality simulation can be used to check the robustness of data analysis findings and learn about the impact of data quality contaminations on classification. This package helps to add contaminations (noise, missing values, outliers, low variance, irrelevant features, class swap (inconsistency), class imbalance and decrease in data volume) to data and then evaluate the simulated data sets for classification accuracy. As a lightweight solution simulation runs can be set up with no or minimal up-front effort.
License: GPL-2
LazyData: TRUE
Imports: DMwR, reshape2, ggplot2, methods, stats, caret, doParallel, foreach
Suggests: gbm, testthat, preprocomb, preproviz, knitr, rmarkdown
URL: https://github.com/mvattulainen/preprosim
BugReports: https://github.com/mvattulainen/preprosim/issues
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-28 04:39:33 UTC; Markus
Author: Markus Vattulainen [aut, cre]
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-28 08:18:24

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Package MVar.pt updated to version 1.8 with previous version 1.7 dated 2016-04-14

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), analise de multiplos fatores (MFA), para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MVar.pt versions 1.7 dated 2016-04-14 and 1.8 dated 2016-05-28

 DESCRIPTION            |    8 ++++----
 MD5                    |   10 ++++++----
 R/CoefVar.R            |only
 R/NormData.R           |   16 ++++++++++------
 R/Plot.MFA.R           |    4 ++--
 man/CoefVar.Rd         |only
 man/MVar.pt-package.Rd |    4 ++--
 7 files changed, 24 insertions(+), 18 deletions(-)

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New package evclust with initial version 1.0.1
Package: evclust
Type: Package
Title: Evidential Clustering
Version: 1.0.1
Date: 2016-05-15
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
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.
Depends: R (>= 3.1.0),
Imports: FNN, R.utils, limSolve, Matrix
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Suggests: knitr,rmarkdown
NeedsCompilation: no
Packaged: 2016-05-28 03:27:49 UTC; Thierry
Repository: CRAN
Date/Publication: 2016-05-28 08:18:28

More information about evclust at CRAN
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Fri, 27 May 2016

Package softclassval updated to version 1.0-20160527 with previous version 1.0-20150416 dated 2015-04-16

Title: Soft Classification Performance Measures
Description: An extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1].
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>

Diff between softclassval versions 1.0-20150416 dated 2015-04-16 and 1.0-20160527 dated 2016-05-27

 softclassval-1.0-20150416/softclassval/tests/tests.Rout             |only
 softclassval-1.0-20160527/softclassval/DESCRIPTION                  |   13 +-
 softclassval-1.0-20160527/softclassval/MD5                          |   32 ++---
 softclassval-1.0-20160527/softclassval/NAMESPACE                    |    4 
 softclassval-1.0-20160527/softclassval/R/hardclasses.R              |   29 ++---
 softclassval-1.0-20160527/softclassval/R/operators.R                |   57 +++++-----
 softclassval-1.0-20160527/softclassval/man/checkrp.Rd               |    2 
 softclassval-1.0-20160527/softclassval/man/dev.Rd                   |    4 
 softclassval-1.0-20160527/softclassval/man/factor2matrix.Rd         |    2 
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 softclassval-1.0-20160527/softclassval/man/hardclasses.Rd           |    2 
 softclassval-1.0-20160527/softclassval/man/nsamples.Rd              |    2 
 softclassval-1.0-20160527/softclassval/man/operators.Rd             |    4 
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 softclassval-1.0-20160527/softclassval/man/postproc.Rd              |    4 
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New package rslurm with initial version 0.3.0
Package: rslurm
Type: Package
Title: Submit R Calculations to a 'SLURM' Cluster
Description: Functions that simplify the R interface the 'SLURM' cluster workload manager, and automate the process of dividing a parallel calculation across cluster nodes.
Version: 0.3.0
License: GPL-3
URL: https://github.com/SESYNC-ci/rslurm
BugReports: https://github.com/SESYNC-ci/rslurm/issues
Authors@R: c(person('Philippe', 'Marchand', email = 'pmarchand@sesync.org', role = c('aut', 'cre')), person('Mike', 'Smorul', role = 'ctb'))
Depends: R (>= 3.2.0)
Imports: parallel, whisker (>= 0.3)
RoxygenNote: 5.0.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-27 23:17:32 UTC; pmarchand
Author: Philippe Marchand [aut, cre], Mike Smorul [ctb]
Maintainer: Philippe Marchand <pmarchand@sesync.org>
Repository: CRAN
Date/Publication: 2016-05-28 01:55:25

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Package arrayhelpers updated to version 1.0-20160527 with previous version 0.76-20120816 dated 2012-08-17

Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>

Diff between arrayhelpers versions 0.76-20120816 dated 2012-08-17 and 1.0-20160527 dated 2016-05-27

 arrayhelpers-0.76-20120816/arrayhelpers/R/validate.R                |only
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 arrayhelpers-1.0-20160527/arrayhelpers/DESCRIPTION                  |   31 +--
 arrayhelpers-1.0-20160527/arrayhelpers/MD5                          |   53 ++---
 arrayhelpers-1.0-20160527/arrayhelpers/NAMESPACE                    |   17 +
 arrayhelpers-1.0-20160527/arrayhelpers/R/arrayhelpers.R             |   34 +--
 arrayhelpers-1.0-20160527/arrayhelpers/R/colSums.R                  |    8 
 arrayhelpers-1.0-20160527/arrayhelpers/R/countrows.R                |    3 
 arrayhelpers-1.0-20160527/arrayhelpers/R/rowsum.R                   |    2 
 arrayhelpers-1.0-20160527/arrayhelpers/R/slice.R                    |   40 ++++
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 arrayhelpers-1.0-20160527/arrayhelpers/man/arrayhelpers-package.Rd  |   12 +
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 arrayhelpers-1.0-20160527/arrayhelpers/man/colSums.Rd               |   97 ++++------
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 arrayhelpers-1.0-20160527/arrayhelpers/man/ensuredim.Rd             |   24 +-
 arrayhelpers-1.0-20160527/arrayhelpers/man/groupsum.Rd              |   35 +--
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 arrayhelpers-1.0-20160527/arrayhelpers/man/slice.Rd                 |   32 +--
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New package dataone with initial version 2.0.0
Package: dataone
Version: 2.0.0
Date: 2016-05-24
Title: R Interface to the DataONE REST API
Authors@R: c( person("Matthew B.", "Jones", role = c("aut", "cre"), email = "jones@nceas.ucsb.edu"), person("Peter", "Slaughter", role = "aut", email = "slaughter@nceas.ucsb.edu"), person("Rob", "Nahf", role = "aut", email = "rnahf@unm.edu"), person("Carl", "Boettiger", role = "aut", email = "cboettig@gmail.com"), person("Chris", "Jones", role = "aut", email = "cjones@nceas.ucsb.edu"), person("Jordan", "Read", role = "aut", email = "jread@usgs.gov"), person("Lauren", "Walker", role = "aut", email = "walker@nceas.ucsb.edu"), person("Edmund", "Hart", role = "aut", email = "edmund.m.hart@gmail.com"), person("Scott", "Chamberlain", role = "aut", email = "myrmecocystus@gmail.com"), person("Regents of the University of California", role = c("cph")))
VignetteBuilder: knitr
Description: Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.
Depends: R (>= 3.1.1),
Suggests: knitr, testthat, digest, openssl (>= 0.9.3)
Imports: XML (>= 3.95-0.1), hash, httr, methods, stringr, datapack, plyr, parsedate, uuid, base64enc, jsonlite
License: Apache License 2.0
URL: https://github.com/DataONEorg/rdataone
BugReports: https://github.com/DataONEorg/rdataone/issues
Collate: 'AbstractTableDescriber.R' 'auth_request.R' 'D1Node.R' 'AuthenticationManager.R' 'CNode.R' 'CertificateManager.R' 'D1Object.R' 'MNode.R' 'D1Client.R' 'EMLParser.R' 'dataone-package.R' 'yyy.R' 'zzz.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-27 18:24:44 UTC; jones
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Rob Nahf [aut], Carl Boettiger [aut], Chris Jones [aut], Jordan Read [aut], Lauren Walker [aut], Edmund Hart [aut], Scott Chamberlain [aut], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
X-CRAN-Comment: Archived on 2014-08-29 as dataonelibs was.
Repository: CRAN
Date/Publication: 2016-05-28 01:52:05

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Package BinNor updated to version 2.1 with previous version 2.0 dated 2012-05-24

Title: Simultaneous Generation of Multivariate Binary and Normal Variates
Description: Generating multiple binary and normal variables simultaneously given marginal characteristics and association structure based on the methodology proposed by Demirtas and Doganay (2012).
Author: Anup Amatya, Hakan Demirtas
Maintainer: Anup Amatya <aamatya@nmsu.edu>

Diff between BinNor versions 2.0 dated 2012-05-24 and 2.1 dated 2016-05-27

 DESCRIPTION           |   18 ++++++++----------
 MD5                   |    6 +++---
 NAMESPACE             |   15 +++------------
 man/BinNor-package.Rd |    9 +++++----
 4 files changed, 19 insertions(+), 29 deletions(-)

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Package VGAM updated to version 1.0-2 with previous version 1.0-1 dated 2016-03-15

Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of statistical regression models. At the heart of it are the vector generalized linear and additive model (VGLM/VGAM) classes, and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and VGAM package. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>

Diff between VGAM versions 1.0-1 dated 2016-03-15 and 1.0-2 dated 2016-05-27

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 VGAM-1.0-2/VGAM/R/attrassign.R                   |   36 
 VGAM-1.0-2/VGAM/R/bAIC.q                         |    2 
 VGAM-1.0-2/VGAM/R/build.terms.vlm.q              |    8 
 VGAM-1.0-2/VGAM/R/calibrate.q                    |    4 
 VGAM-1.0-2/VGAM/R/cao.R                          |   12 
 VGAM-1.0-2/VGAM/R/cao.fit.q                      |  124 
 VGAM-1.0-2/VGAM/R/coef.vlm.q                     |    4 
 VGAM-1.0-2/VGAM/R/confint.vlm.R                  |   20 
 VGAM-1.0-2/VGAM/R/cqo.R                          |    8 
 VGAM-1.0-2/VGAM/R/cqo.fit.q                      |   39 
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 VGAM-1.0-2/VGAM/R/effects.vglm.q                 |    2 
 VGAM-1.0-2/VGAM/R/family.actuary.R               | 1219 ++--
 VGAM-1.0-2/VGAM/R/family.aunivariate.R           | 1064 ++++
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 VGAM-1.0-2/VGAM/R/family.normal.R                |  317 -
 VGAM-1.0-2/VGAM/R/family.others.R                |  463 +
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 VGAM-1.0-2/VGAM/R/family.qreg.R                  |  376 -
 VGAM-1.0-2/VGAM/R/family.rcim.R                  |   26 
 VGAM-1.0-2/VGAM/R/family.rcqo.R                  |   16 
 VGAM-1.0-2/VGAM/R/family.robust.R                |   18 
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 VGAM-1.0-2/VGAM/R/family.survival.R              |   24 
 VGAM-1.0-2/VGAM/R/family.ts.R                    | 1051 ++--
 VGAM-1.0-2/VGAM/R/family.univariate.R            | 1581 ++----
 VGAM-1.0-2/VGAM/R/family.vglm.R                  |    4 
 VGAM-1.0-2/VGAM/R/family.zeroinf.R               | 5779 +++++++++++++----------
 VGAM-1.0-2/VGAM/R/fittedvlm.R                    |    2 
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 VGAM-1.0-2/VGAM/R/vglm.R                         |   17 
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 VGAM-1.0-2/VGAM/R/vlm.R                          |    4 
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 VGAM-1.0-2/VGAM/man/calibrate.qrrvglm.control.Rd |    2 
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 222 files changed, 10636 insertions(+), 7589 deletions(-)

More information about VGAM at CRAN
Permanent link

New package vembedr with initial version 0.1.0
Package: vembedr
Title: Functions to Embed Video in HTML
Version: 0.1.0
Authors@R: c( person("Ian", "Lyttle", email = "ian.lyttle@schneider-electric.com", role = c("aut", "cre", "cph")) )
Description: A set of functions for generating HTML to embed hosted video in your R Markdown documents or Shiny apps.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: htmltools, httr, stringr
RoxygenNote: 5.0.1
URL: https://github.com/ijlyttle/vembedr
BugReports: https://github.com/ijlyttle/vembedr/issues
Suggests: testthat, knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-27 16:20:09 UTC; ijlyttle
Author: Ian Lyttle [aut, cre, cph]
Maintainer: Ian Lyttle <ian.lyttle@schneider-electric.com>
Repository: CRAN
Date/Publication: 2016-05-27 18:38:56

More information about vembedr at CRAN
Permanent link

Package TipDatingBeast updated to version 1.0-2 with previous version 0.1-6 dated 2015-07-29

Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for Phylogenetic Analysis)
Description: Assist performing tip-dating of phylogenetic trees with BEAST.
Author: Adrien Rieux, Camilo Khatchikian
Maintainer: Camilo Khatchikian <ckhatchikian@gmail.com>

Diff between TipDatingBeast versions 0.1-6 dated 2015-07-29 and 1.0-2 dated 2016-05-27

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 TipDatingBeast-1.0-2/TipDatingBeast/DESCRIPTION                              |   13 
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 TipDatingBeast-1.0-2/TipDatingBeast/NAMESPACE                                |    7 
 TipDatingBeast-1.0-2/TipDatingBeast/R/ListTaxa.R                             |   97 ++-
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 TipDatingBeast-1.0-2/TipDatingBeast/R/RandomCluster.R                        |  258 ++++++---
 TipDatingBeast-1.0-2/TipDatingBeast/R/RandomDates.R                          |  197 +++++-
 TipDatingBeast-1.0-2/TipDatingBeast/R/TaxaOut.R                              |  279 ++++++---
 TipDatingBeast-1.0-2/TipDatingBeast/R/TaxonOut.R                             |  285 +++++++---
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 34 files changed, 933 insertions(+), 371 deletions(-)

More information about TipDatingBeast at CRAN
Permanent link

Package stringi updated to version 1.1.1 with previous version 1.0-1 dated 2015-10-22

Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code); IBM and other contributors (ICU4C 55.1 source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between stringi versions 1.0-1 dated 2015-10-22 and 1.1.1 dated 2016-05-27

 DESCRIPTION                              |   17 
 INSTALL                                  |   10 
 LICENSE                                  |    6 
 MD5                                      |  541 +++++++++++++++----------------
 NAMESPACE                                |   10 
 NEWS                                     |   34 +
 R/ICU_settings.R                         |    2 
 R/compare.R                              |    2 
 R/draft_encdetect.R                      |    2 
 R/draft_files.R                          |    2 
 R/encoding.R                             |    4 
 R/encoding_conversion.R                  |    2 
 R/encoding_detection.R                   |    2 
 R/encoding_management.R                  |    2 
 R/escape.R                               |    2 
 R/install.R                              |    2 
 R/internal_prepare_arg.R                 |   19 -
 R/internal_test.R                        |    2 
 R/join.R                                 |   76 +++-
 R/length.R                               |    2 
 R/locale.R                               |   34 -
 R/locale_management.R                    |    2 
 R/opts.R                                 |    2 
 R/pad.R                                  |    2 
 R/random.R                               |    2 
 R/reverse.R                              |    2 
 R/search.R                               |    9 
 R/search_count_4.R                       |    2 
 R/search_count_bound.R                   |    2 
 R/search_detect_4.R                      |   26 -
 R/search_extract_4.R                     |    2 
 R/search_extract_bound.R                 |    2 
 R/search_locate_4.R                      |    2 
 R/search_locate_bound.R                  |    2 
 R/search_match_4.R                       |    2 
 R/search_replace_4.R                     |    4 
 R/search_replace_na.R                    |    2 
 R/search_split_4.R                       |    2 
 R/search_split_bound.R                   |    6 
 R/search_startsendswith_4.R              |   14 
 R/search_subset_4.R                      |  114 +++++-
 R/sort.R                                 |    2 
 R/stats.R                                |    2 
 R/stringi-package.R                      |   25 -
 R/sub.R                                  |   41 +-
 R/time_calendar.R                        |    2 
 R/time_format.R                          |    2 
 R/time_symbols.R                         |    2 
 R/time_zone.R                            |    2 
 R/todo_charclass.R                       |    2 
 R/todo_justify.R                         |    2 
 R/todo_rbnf.R                            |    2 
 R/todo_search_in.R                       |    2 
 R/todo_split.R                           |    2 
 R/trans_casemap.R                        |    2 
 R/trans_normalization.R                  |    2 
 R/trans_other.R                          |    2 
 R/trans_transliterate.R                  |    2 
 R/trim.R                                 |    2 
 R/utils.R                                |    2 
 R/wrap.R                                 |    2 
 configure                                |   18 -
 inst/AUTHORS                             |    3 
 inst/CITATION                            |   11 
 man/oper_comparison.Rd                   |   41 --
 man/oper_plus.Rd                         |    3 
 man/stri_compare.Rd                      |   43 --
 man/stri_count.Rd                        |    8 
 man/stri_count_boundaries.Rd             |   73 ----
 man/stri_datetime_add.Rd                 |   18 -
 man/stri_datetime_create.Rd              |   17 
 man/stri_datetime_fields.Rd              |   17 
 man/stri_datetime_format.Rd              |   17 
 man/stri_datetime_fstr.Rd                |   17 
 man/stri_datetime_now.Rd                 |   16 
 man/stri_datetime_symbols.Rd             |   17 
 man/stri_detect.Rd                       |   33 -
 man/stri_dup.Rd                          |    6 
 man/stri_duplicated.Rd                   |   91 +----
 man/stri_enc_detect.Rd                   |   12 
 man/stri_enc_detect2.Rd                  |   54 ---
 man/stri_enc_fromutf32.Rd                |   12 
 man/stri_enc_info.Rd                     |    7 
 man/stri_enc_isascii.Rd                  |   12 
 man/stri_enc_isutf16.Rd                  |   10 
 man/stri_enc_isutf8.Rd                   |   12 
 man/stri_enc_list.Rd                     |    7 
 man/stri_enc_mark.Rd                     |    7 
 man/stri_enc_set.Rd                      |    6 
 man/stri_enc_toascii.Rd                  |   12 
 man/stri_enc_tonative.Rd                 |   12 
 man/stri_enc_toutf32.Rd                  |   12 
 man/stri_enc_toutf8.Rd                   |   14 
 man/stri_encode.Rd                       |   12 
 man/stri_escape_unicode.Rd               |    3 
 man/stri_extract.Rd                      |   19 -
 man/stri_extract_boundaries.Rd           |   85 ----
 man/stri_flatten.Rd                      |    7 
 man/stri_info.Rd                         |    2 
 man/stri_install.Rd                      |    3 
 man/stri_isempty.Rd                      |    7 
 man/stri_join.Rd                         |   22 -
 man/stri_join_list.Rd                    |only
 man/stri_length.Rd                       |    7 
 man/stri_list2matrix.Rd                  |    3 
 man/stri_locale_info.Rd                  |    8 
 man/stri_locale_list.Rd                  |    7 
 man/stri_locale_set.Rd                   |    6 
 man/stri_locate.Rd                       |   20 -
 man/stri_locate_boundaries.Rd            |   99 +----
 man/stri_match.Rd                        |   25 -
 man/stri_numbytes.Rd                     |    7 
 man/stri_opts_brkiter.Rd                 |   23 -
 man/stri_opts_collator.Rd                |   47 --
 man/stri_opts_fixed.Rd                   |    4 
 man/stri_opts_regex.Rd                   |    4 
 man/stri_order.Rd                        |   45 --
 man/stri_pad.Rd                          |    2 
 man/stri_rand_lipsum.Rd                  |    5 
 man/stri_rand_shuffle.Rd                 |    5 
 man/stri_rand_strings.Rd                 |    5 
 man/stri_read_lines.Rd                   |    4 
 man/stri_read_raw.Rd                     |    4 
 man/stri_replace.Rd                      |   14 
 man/stri_replace_na.Rd                   |   23 -
 man/stri_reverse.Rd                      |    3 
 man/stri_split.Rd                        |   11 
 man/stri_split_boundaries.Rd             |   80 +---
 man/stri_split_lines.Rd                  |   32 -
 man/stri_startsendswith.Rd               |   23 -
 man/stri_stats_general.Rd                |    3 
 man/stri_stats_latex.Rd                  |    3 
 man/stri_sub.Rd                          |   44 --
 man/stri_subset.Rd                       |   72 ++--
 man/stri_timezone_info.Rd                |   18 -
 man/stri_timezone_list.Rd                |   18 -
 man/stri_timezone_set.Rd                 |   20 -
 man/stri_trans_casemap.Rd                |   83 +---
 man/stri_trans_char.Rd                   |   19 -
 man/stri_trans_general.Rd                |   19 -
 man/stri_trans_list.Rd                   |   19 -
 man/stri_trans_nf.Rd                     |   13 
 man/stri_trim.Rd                         |   24 -
 man/stri_unescape_unicode.Rd             |    3 
 man/stri_unique.Rd                       |   46 --
 man/stri_width.Rd                        |    6 
 man/stri_wrap.Rd                         |   69 ---
 man/stri_write_lines.Rd                  |    4 
 man/stringi-arguments.Rd                 |   37 +-
 man/stringi-encoding.Rd                  |   53 +--
 man/stringi-locale.Rd                    |  104 ++---
 man/stringi-package.Rd                   |   41 +-
 man/stringi-search-boundaries.Rd         |   84 +---
 man/stringi-search-charclass.Rd          |   25 -
 man/stringi-search-coll.Rd               |   65 +--
 man/stringi-search-fixed.Rd              |   22 -
 man/stringi-search-regex.Rd              |   29 -
 man/stringi-search.Rd                    |  166 +--------
 src/stri_ICU_settings.cpp                |    2 
 src/stri_TODO_justify.cpp                |    2 
 src/stri_TODO_splitpos.cpp               |    2 
 src/stri_TODO_uchar.cpp                  |    2 
 src/stri_brkiter.cpp                     |    2 
 src/stri_brkiter.h                       |    2 
 src/stri_bytesearch_matcher.h            |    2 
 src/stri_collator.cpp                    |    2 
 src/stri_common.cpp                      |    2 
 src/stri_compare.cpp                     |    2 
 src/stri_container_base.cpp              |    2 
 src/stri_container_base.h                |    2 
 src/stri_container_bytesearch.cpp        |    2 
 src/stri_container_bytesearch.h          |    2 
 src/stri_container_charclass.h           |    2 
 src/stri_container_double.h              |    2 
 src/stri_container_integer.h             |    2 
 src/stri_container_listint.cpp           |    2 
 src/stri_container_listint.h             |    2 
 src/stri_container_listraw.cpp           |    2 
 src/stri_container_listraw.h             |    2 
 src/stri_container_listutf8.cpp          |    2 
 src/stri_container_listutf8.h            |    2 
 src/stri_container_logical.h             |    2 
 src/stri_container_regex.cpp             |    2 
 src/stri_container_regex.h               |    2 
 src/stri_container_usearch.cpp           |    2 
 src/stri_container_usearch.h             |    2 
 src/stri_container_utf16.cpp             |    2 
 src/stri_container_utf16.h               |    2 
 src/stri_container_utf8.cpp              |    2 
 src/stri_container_utf8.h                |    2 
 src/stri_container_utf8_indexable.cpp    |    2 
 src/stri_container_utf8_indexable.h      |    2 
 src/stri_encoding_conversion.cpp         |    2 
 src/stri_encoding_detection.cpp          |    2 
 src/stri_encoding_management.cpp         |    2 
 src/stri_escape.cpp                      |    2 
 src/stri_exception.cpp                   |    2 
 src/stri_exception.h                     |    2 
 src/stri_exports.h                       |   30 -
 src/stri_external.h                      |    2 
 src/stri_interval.h                      |    2 
 src/stri_intvec.h                        |    2 
 src/stri_join.cpp                        |   50 ++
 src/stri_length.cpp                      |    2 
 src/stri_macros.h                        |   12 
 src/stri_messages.h                      |    7 
 src/stri_pad.cpp                         |    2 
 src/stri_prepare_arg.cpp                 |    2 
 src/stri_random.cpp                      |    2 
 src/stri_reverse.cpp                     |    2 
 src/stri_search_boundaries_count.cpp     |    2 
 src/stri_search_boundaries_extract.cpp   |    2 
 src/stri_search_boundaries_locate.cpp    |    2 
 src/stri_search_boundaries_split.cpp     |    2 
 src/stri_search_class_count.cpp          |    2 
 src/stri_search_class_detect.cpp         |    9 
 src/stri_search_class_extract.cpp        |    2 
 src/stri_search_class_locate.cpp         |    2 
 src/stri_search_class_replace.cpp        |   32 +
 src/stri_search_class_split.cpp          |    2 
 src/stri_search_class_startsendswith.cpp |    2 
 src/stri_search_class_subset.cpp         |   84 ++++
 src/stri_search_class_trim.cpp           |    2 
 src/stri_search_coll_count.cpp           |    2 
 src/stri_search_coll_detect.cpp          |   11 
 src/stri_search_coll_extract.cpp         |    2 
 src/stri_search_coll_locate.cpp          |    2 
 src/stri_search_coll_replace.cpp         |   30 +
 src/stri_search_coll_split.cpp           |    2 
 src/stri_search_coll_startsendswith.cpp  |    2 
 src/stri_search_coll_subset.cpp          |   80 ++++
 src/stri_search_common.cpp               |    2 
 src/stri_search_fixed_count.cpp          |    2 
 src/stri_search_fixed_detect.cpp         |   11 
 src/stri_search_fixed_extract.cpp        |    2 
 src/stri_search_fixed_locate.cpp         |    2 
 src/stri_search_fixed_replace.cpp        |   27 +
 src/stri_search_fixed_split.cpp          |    2 
 src/stri_search_fixed_startsendswith.cpp |    2 
 src/stri_search_fixed_subset.cpp         |   73 ++++
 src/stri_search_in.cpp                   |    2 
 src/stri_search_other_replace.cpp        |    2 
 src/stri_search_other_split.cpp          |    2 
 src/stri_search_regex_count.cpp          |    9 
 src/stri_search_regex_detect.cpp         |   16 
 src/stri_search_regex_extract.cpp        |   17 
 src/stri_search_regex_locate.cpp         |   15 
 src/stri_search_regex_match.cpp          |   19 -
 src/stri_search_regex_replace.cpp        |   34 +
 src/stri_search_regex_split.cpp          |    2 
 src/stri_search_regex_subset.cpp         |   93 +++++
 src/stri_sort.cpp                        |    2 
 src/stri_stats.cpp                       |    2 
 src/stri_string8.h                       |    8 
 src/stri_string8buf.h                    |    2 
 src/stri_stringi.cpp                     |  363 ++++++++++----------
 src/stri_stringi.h                       |    2 
 src/stri_sub.cpp                         |   33 +
 src/stri_test.cpp                        |    2 
 src/stri_time_calendar.cpp               |    2 
 src/stri_time_format.cpp                 |    2 
 src/stri_time_symbols.cpp                |    2 
 src/stri_time_zone.cpp                   |    2 
 src/stri_trans_casemap.cpp               |    2 
 src/stri_trans_normalization.cpp         |    2 
 src/stri_trans_other.cpp                 |    2 
 src/stri_trans_transliterate.cpp         |    2 
 src/stri_ucnv.cpp                        |    2 
 src/stri_ucnv.h                          |    2 
 src/stri_uloc.cpp                        |    2 
 src/stri_utils.cpp                       |    2 
 src/stri_wrap.cpp                        |    2 
 272 files changed, 2268 insertions(+), 2476 deletions(-)

More information about stringi at CRAN
Permanent link

Package RcppArmadillo updated to version 0.7.100.3.0 with previous version 0.6.700.6.0 dated 2016-05-05

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.6.700.6.0 dated 2016-05-05 and 0.7.100.3.0 dated 2016-05-27

 ChangeLog                                                         |   25 
 DESCRIPTION                                                       |    8 
 MD5                                                               |  392 
 configure                                                         | 3934 +++++++++-
 configure.ac                                                      |only
 inst/NEWS.Rd                                                      |   20 
 inst/doc/RcppArmadillo-intro.pdf                                  |binary
 inst/doc/RcppArmadillo-unitTests.pdf                              |binary
 inst/include/RcppArmadilloLapack.h.in                             |    6 
 inst/include/armadillo                                            |   46 
 inst/include/armadillo_bits/Cube_bones.hpp                        |    6 
 inst/include/armadillo_bits/Cube_meat.hpp                         |   68 
 inst/include/armadillo_bits/GenCube_bones.hpp                     |    4 
 inst/include/armadillo_bits/Gen_bones.hpp                         |    4 
 inst/include/armadillo_bits/Mat_meat.hpp                          |    8 
 inst/include/armadillo_bits/Proxy.hpp                             |  242 
 inst/include/armadillo_bits/ProxyCube.hpp                         |   38 
 inst/include/armadillo_bits/SpMat_bones.hpp                       |    2 
 inst/include/armadillo_bits/SpMat_meat.hpp                        |   12 
 inst/include/armadillo_bits/SpProxy.hpp                           |   28 
 inst/include/armadillo_bits/arma_cmath.hpp                        |   12 
 inst/include/armadillo_bits/arma_config.hpp                       |    9 
 inst/include/armadillo_bits/arma_rng.hpp                          |    1 
 inst/include/armadillo_bits/arma_version.hpp                      |    8 
 inst/include/armadillo_bits/auxlib_meat.hpp                       |   98 
 inst/include/armadillo_bits/compiler_setup.hpp                    |  104 
 inst/include/armadillo_bits/config.hpp                            |   14 
 inst/include/armadillo_bits/config.hpp.cmake                      |   14 
 inst/include/armadillo_bits/debug.hpp                             |  123 
 inst/include/armadillo_bits/def_lapack.hpp                        |   72 
 inst/include/armadillo_bits/def_superlu.hpp                       |    8 
 inst/include/armadillo_bits/diagmat_proxy.hpp                     |    6 
 inst/include/armadillo_bits/diagview_meat.hpp                     |   12 
 inst/include/armadillo_bits/diskio_meat.hpp                       |    8 
 inst/include/armadillo_bits/eGlueCube_bones.hpp                   |    6 
 inst/include/armadillo_bits/eGlue_bones.hpp                       |    8 
 inst/include/armadillo_bits/eOpCube_bones.hpp                     |    6 
 inst/include/armadillo_bits/eOp_bones.hpp                         |    8 
 inst/include/armadillo_bits/eglue_core_meat.hpp                   |   42 
 inst/include/armadillo_bits/eop_aux.hpp                           |   40 
 inst/include/armadillo_bits/eop_core_bones.hpp                    |    3 
 inst/include/armadillo_bits/eop_core_meat.hpp                     |   31 
 inst/include/armadillo_bits/fn_accu.hpp                           |   22 
 inst/include/armadillo_bits/fn_all.hpp                            |    9 
 inst/include/armadillo_bits/fn_any.hpp                            |    9 
 inst/include/armadillo_bits/fn_approx_equal.hpp                   |    4 
 inst/include/armadillo_bits/fn_as_scalar.hpp                      |   27 
 inst/include/armadillo_bits/fn_chol.hpp                           |    3 
 inst/include/armadillo_bits/fn_clamp.hpp                          |    2 
 inst/include/armadillo_bits/fn_conv.hpp                           |    2 
 inst/include/armadillo_bits/fn_conv_to.hpp                        |   32 
 inst/include/armadillo_bits/fn_cor.hpp                            |    4 
 inst/include/armadillo_bits/fn_cov.hpp                            |    4 
 inst/include/armadillo_bits/fn_cross.hpp                          |    3 
 inst/include/armadillo_bits/fn_cumprod.hpp                        |    6 
 inst/include/armadillo_bits/fn_cumsum.hpp                         |    6 
 inst/include/armadillo_bits/fn_det.hpp                            |   16 
 inst/include/armadillo_bits/fn_diagmat.hpp                        |    6 
 inst/include/armadillo_bits/fn_diagvec.hpp                        |    3 
 inst/include/armadillo_bits/fn_diff.hpp                           |    4 
 inst/include/armadillo_bits/fn_dot.hpp                            |   20 
 inst/include/armadillo_bits/fn_eig_gen.hpp                        |    3 
 inst/include/armadillo_bits/fn_eig_pair.hpp                       |    3 
 inst/include/armadillo_bits/fn_eig_sym.hpp                        |    5 
 inst/include/armadillo_bits/fn_eigs_gen.hpp                       |    5 
 inst/include/armadillo_bits/fn_eigs_sym.hpp                       |    5 
 inst/include/armadillo_bits/fn_elem.hpp                           |  143 
 inst/include/armadillo_bits/fn_eps.hpp                            |   21 
 inst/include/armadillo_bits/fn_expmat.hpp                         |    3 
 inst/include/armadillo_bits/fn_eye.hpp                            |    8 
 inst/include/armadillo_bits/fn_fft.hpp                            |    8 
 inst/include/armadillo_bits/fn_fft2.hpp                           |    6 
 inst/include/armadillo_bits/fn_find.hpp                           |   12 
 inst/include/armadillo_bits/fn_find_unique.hpp                    |    4 
 inst/include/armadillo_bits/fn_flip.hpp                           |    4 
 inst/include/armadillo_bits/fn_hist.hpp                           |    5 
 inst/include/armadillo_bits/fn_histc.hpp                          |    4 
 inst/include/armadillo_bits/fn_inv.hpp                            |    9 
 inst/include/armadillo_bits/fn_join.hpp                           |   14 
 inst/include/armadillo_bits/fn_kmeans.hpp                         |   10 
 inst/include/armadillo_bits/fn_kron.hpp                           |   13 
 inst/include/armadillo_bits/fn_logmat.hpp                         |    2 
 inst/include/armadillo_bits/fn_max.hpp                            |   30 
 inst/include/armadillo_bits/fn_mean.hpp                           |   21 
 inst/include/armadillo_bits/fn_median.hpp                         |    8 
 inst/include/armadillo_bits/fn_min.hpp                            |   29 
 inst/include/armadillo_bits/fn_misc.hpp                           |   26 
 inst/include/armadillo_bits/fn_nonzeros.hpp                       |    4 
 inst/include/armadillo_bits/fn_norm.hpp                           |   12 
 inst/include/armadillo_bits/fn_normalise.hpp                      |    4 
 inst/include/armadillo_bits/fn_numel.hpp                          |    7 
 inst/include/armadillo_bits/fn_ones.hpp                           |   12 
 inst/include/armadillo_bits/fn_pinv.hpp                           |    3 
 inst/include/armadillo_bits/fn_princomp.hpp                       |    3 
 inst/include/armadillo_bits/fn_prod.hpp                           |   15 
 inst/include/armadillo_bits/fn_randg.hpp                          |   16 
 inst/include/armadillo_bits/fn_randi.hpp                          |   12 
 inst/include/armadillo_bits/fn_randn.hpp                          |   12 
 inst/include/armadillo_bits/fn_randu.hpp                          |   14 
 inst/include/armadillo_bits/fn_rank.hpp                           |    6 
 inst/include/armadillo_bits/fn_regspace.hpp                       |    3 
 inst/include/armadillo_bits/fn_repmat.hpp                         |    4 
 inst/include/armadillo_bits/fn_schur.hpp                          |    5 
 inst/include/armadillo_bits/fn_shift.hpp                          |    2 
 inst/include/armadillo_bits/fn_shuffle.hpp                        |    4 
 inst/include/armadillo_bits/fn_size.hpp                           |   14 
 inst/include/armadillo_bits/fn_solve.hpp                          |    8 
 inst/include/armadillo_bits/fn_sort.hpp                           |    6 
 inst/include/armadillo_bits/fn_sort_index.hpp                     |    6 
 inst/include/armadillo_bits/fn_speye.hpp                          |    6 
 inst/include/armadillo_bits/fn_spones.hpp                         |    3 
 inst/include/armadillo_bits/fn_sprandn.hpp                        |    7 
 inst/include/armadillo_bits/fn_sprandu.hpp                        |    7 
 inst/include/armadillo_bits/fn_spsolve.hpp                        |    3 
 inst/include/armadillo_bits/fn_sqrtmat.hpp                        |    2 
 inst/include/armadillo_bits/fn_stddev.hpp                         |    8 
 inst/include/armadillo_bits/fn_strans.hpp                         |    6 
 inst/include/armadillo_bits/fn_sum.hpp                            |   29 
 inst/include/armadillo_bits/fn_svd.hpp                            |    5 
 inst/include/armadillo_bits/fn_svds.hpp                           |   14 
 inst/include/armadillo_bits/fn_syl_lyap.hpp                       |    5 
 inst/include/armadillo_bits/fn_symmat.hpp                         |    6 
 inst/include/armadillo_bits/fn_toeplitz.hpp                       |   11 
 inst/include/armadillo_bits/fn_trace.hpp                          |   10 
 inst/include/armadillo_bits/fn_trans.hpp                          |    9 
 inst/include/armadillo_bits/fn_trapz.hpp                          |    2 
 inst/include/armadillo_bits/fn_trig.hpp                           |   26 
 inst/include/armadillo_bits/fn_trimat.hpp                         |    4 
 inst/include/armadillo_bits/fn_trunc_exp.hpp                      |    6 
 inst/include/armadillo_bits/fn_trunc_log.hpp                      |    5 
 inst/include/armadillo_bits/fn_unique.hpp                         |    3 
 inst/include/armadillo_bits/fn_var.hpp                            |   11 
 inst/include/armadillo_bits/fn_vectorise.hpp                      |    5 
 inst/include/armadillo_bits/fn_zeros.hpp                          |   14 
 inst/include/armadillo_bits/glue_cross_meat.hpp                   |    4 
 inst/include/armadillo_bits/glue_max_meat.hpp                     |   10 
 inst/include/armadillo_bits/glue_min_meat.hpp                     |    8 
 inst/include/armadillo_bits/glue_mixed_meat.hpp                   |   34 
 inst/include/armadillo_bits/glue_relational_meat.hpp              |   10 
 inst/include/armadillo_bits/glue_solve_meat.hpp                   |    4 
 inst/include/armadillo_bits/glue_times_meat.hpp                   |    6 
 inst/include/armadillo_bits/include_superlu.hpp                   |   99 
 inst/include/armadillo_bits/newarp_DenseGenMatProd_bones.hpp      |only
 inst/include/armadillo_bits/newarp_DenseGenMatProd_meat.hpp       |only
 inst/include/armadillo_bits/newarp_DoubleShiftQR_bones.hpp        |only
 inst/include/armadillo_bits/newarp_DoubleShiftQR_meat.hpp         |only
 inst/include/armadillo_bits/newarp_EigsSelect.hpp                 |only
 inst/include/armadillo_bits/newarp_GenEigsSolver_bones.hpp        |only
 inst/include/armadillo_bits/newarp_GenEigsSolver_meat.hpp         |only
 inst/include/armadillo_bits/newarp_SortEigenvalue.hpp             |only
 inst/include/armadillo_bits/newarp_SparseGenMatProd_bones.hpp     |only
 inst/include/armadillo_bits/newarp_SparseGenMatProd_meat.hpp      |only
 inst/include/armadillo_bits/newarp_SymEigsSolver_bones.hpp        |only
 inst/include/armadillo_bits/newarp_SymEigsSolver_meat.hpp         |only
 inst/include/armadillo_bits/newarp_TridiagEigen_bones.hpp         |only
 inst/include/armadillo_bits/newarp_TridiagEigen_meat.hpp          |only
 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_bones.hpp |only
 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp  |only
 inst/include/armadillo_bits/newarp_UpperHessenbergQR_bones.hpp    |only
 inst/include/armadillo_bits/newarp_UpperHessenbergQR_meat.hpp     |only
 inst/include/armadillo_bits/newarp_cx_attrib.hpp                  |only
 inst/include/armadillo_bits/op_all_meat.hpp                       |   10 
 inst/include/armadillo_bits/op_any_meat.hpp                       |   10 
 inst/include/armadillo_bits/op_chol_meat.hpp                      |    2 
 inst/include/armadillo_bits/op_clamp_meat.hpp                     |    4 
 inst/include/armadillo_bits/op_cx_scalar_meat.hpp                 |   26 
 inst/include/armadillo_bits/op_diagmat_meat.hpp                   |    8 
 inst/include/armadillo_bits/op_dot_meat.hpp                       |   10 
 inst/include/armadillo_bits/op_fft_meat.hpp                       |    6 
 inst/include/armadillo_bits/op_find_meat.hpp                      |   12 
 inst/include/armadillo_bits/op_find_unique_meat.hpp               |    4 
 inst/include/armadillo_bits/op_htrans_meat.hpp                    |    6 
 inst/include/armadillo_bits/op_inv_meat.hpp                       |    8 
 inst/include/armadillo_bits/op_logmat_meat.hpp                    |    4 
 inst/include/armadillo_bits/op_max_meat.hpp                       |   12 
 inst/include/armadillo_bits/op_median_meat.hpp                    |   10 
 inst/include/armadillo_bits/op_min_meat.hpp                       |   18 
 inst/include/armadillo_bits/op_misc_meat.hpp                      |   18 
 inst/include/armadillo_bits/op_nonzeros_meat.hpp                  |    4 
 inst/include/armadillo_bits/op_norm_meat.hpp                      |   18 
 inst/include/armadillo_bits/op_pinv_meat.hpp                      |    2 
 inst/include/armadillo_bits/op_princomp_meat.hpp                  |    2 
 inst/include/armadillo_bits/op_prod_meat.hpp                      |    4 
 inst/include/armadillo_bits/op_relational_meat.hpp                |   10 
 inst/include/armadillo_bits/op_reshape_meat.hpp                   |    6 
 inst/include/armadillo_bits/op_sort_index_meat.hpp                |    6 
 inst/include/armadillo_bits/op_strans_meat.hpp                    |    6 
 inst/include/armadillo_bits/op_unique_meat.hpp                    |    6 
 inst/include/armadillo_bits/op_vectorise_meat.hpp                 |    6 
 inst/include/armadillo_bits/podarray_meat.hpp                     |    4 
 inst/include/armadillo_bits/sp_auxlib_bones.hpp                   |   17 
 inst/include/armadillo_bits/sp_auxlib_meat.hpp                    |  352 
 inst/include/armadillo_bits/spdiagview_meat.hpp                   |   22 
 inst/include/armadillo_bits/spop_max_meat.hpp                     |   19 
 inst/include/armadillo_bits/spop_mean_meat.hpp                    |   10 
 inst/include/armadillo_bits/spop_min_meat.hpp                     |   19 
 inst/include/armadillo_bits/spop_sum_meat.hpp                     |    4 
 inst/include/armadillo_bits/spop_var_meat.hpp                     |    4 
 inst/include/armadillo_bits/subview_cube_each_meat.hpp            |    2 
 inst/include/armadillo_bits/subview_cube_meat.hpp                 |   18 
 inst/include/armadillo_bits/subview_each_meat.hpp                 |    4 
 inst/include/armadillo_bits/subview_elem1_meat.hpp                |    6 
 inst/include/armadillo_bits/subview_meat.hpp                      |   18 
 inst/include/armadillo_bits/wall_clock_bones.hpp                  |    4 
 inst/include/armadillo_bits/wall_clock_meat.hpp                   |    6 
 inst/include/armadillo_bits/wrapper_lapack.hpp                    |  158 
 inst/include/armadillo_bits/wrapper_superlu.hpp                   |   10 
 207 files changed, 6333 insertions(+), 1195 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link

New package rsq with initial version 0.3
Package: rsq
Title: Coefficient of Determination
Version: 0.3
Date: 2016-05-27
Author: Dabao Zhang
Maintainer: Dabao Zhang <zhangdb@stat.purdue.edu>
Description: Calculates a newly defined coefficient of determination, aka R^2, and coefficient of partial determination, aka partial R^2 by Zhang (2016) for generalized linear models (including quasi models with well defined variance functions). It also avoids overstatement of variation proportion explained by the model or a group of covariates.
Imports: methods
Suggests: stats, MASS
License: GPL-2
NeedsCompilation: no
Packaged: 2016-05-27 14:32:34 UTC; zhangdb
Repository: CRAN
Date/Publication: 2016-05-27 18:48:53

More information about rsq at CRAN
Permanent link

New package plotfunctions with initial version 1.0
Package: plotfunctions
Title: Various Functions to Facilitate Visualization of Data and Analysis
Version: 1.0
Date: 2016-05-26
Author: Jacolien van Rij [aut, cre]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>
Description: When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.
License: GPL (>= 2)
LazyData: true
Depends: R (>= 2.10)
Suggests: knitr, sp
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-27 16:08:42 UTC; jacolien
Repository: CRAN
Date/Publication: 2016-05-27 18:15:05

More information about plotfunctions at CRAN
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Package penalized updated to version 0.9-47 with previous version 0.9-46 dated 2016-04-18

Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>

Diff between penalized versions 0.9-46 dated 2016-04-18 and 0.9-47 dated 2016-05-27

 ChangeLog              |    8 ++++++--
 DESCRIPTION            |    8 ++++----
 MD5                    |   10 +++++-----
 NAMESPACE              |    2 +-
 R/penfit.R             |   14 +++++++++-----
 inst/doc/penalized.pdf |binary
 6 files changed, 25 insertions(+), 17 deletions(-)

More information about penalized at CRAN
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Package oglmx updated to version 2.0.0.0 with previous version 1.0.3 dated 2015-07-31

Title: Estimation of Ordered Generalized Linear Models
Description: Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased. This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects. Wrapper functions to estimate the standard limited dependent variable models are also included.
Author: Nathan Carroll
Maintainer: Nathan Carroll <nathan.carroll@ur.de>

Diff between oglmx versions 1.0.3 dated 2015-07-31 and 2.0.0.0 dated 2016-05-27

 DESCRIPTION                 |   10 
 MD5                         |   18 
 R/oglmx-functions.R         | 1386 +++++++++++++++++++++++++-------------------
 R/oglmx.margins-functions.R |   29 
 build/partial.rdb           |binary
 man/logit.reg.Rd            |    4 
 man/oglmx.Rd                |   21 
 man/ologit.reg.Rd           |   16 
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Permanent link

Package glmmLasso updated to version 1.4.4 with previous version 1.4.3 dated 2016-04-28

Title: Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>

Diff between glmmLasso versions 1.4.3 dated 2016-04-28 and 1.4.4 dated 2016-05-27

 DESCRIPTION      |    8 ++++----
 MD5              |    6 +++---
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 4 files changed, 43 insertions(+), 13 deletions(-)

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Package clusterCrit updated to version 1.2.7 with previous version 1.2.6 dated 2015-08-31

Title: Clustering Indices
Description: Compute clustering validation indices.
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>

Diff between clusterCrit versions 1.2.6 dated 2015-08-31 and 1.2.7 dated 2016-05-27

 DESCRIPTION                                 |    8 ++--
 MD5                                         |   34 +++++++++----------
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New package QFASA with initial version 1.0.0
Package: QFASA
Title: Quantitative Fatty Acid Signature Analysis
Version: 1.0.0
Authors@R: c( person("Sara", "Iverson", email = "Sara.Iverson@dal.ca", role = c("aut")), person("Chris", "Field", email = "field@mathstat.dal.ca", role = c("aut")), person("Don", "Bowen", email = "Don.Bowen@dfo-mpo.gc.ca", role = c("aut")), person("Wade", "Blanchard", email = "wade.blanchard@anu.edu.au", role = c("aut")), person("Connie", "Stewart", email = "connie.stewart@unb.ca", role = c("aut", "cph")), person("Shelly", "Lang", email = "shelley.lang@dfo-mpo.gc.ca", role = c("aut")), person("Justin", "Kamerman", email = "justin.kamerman@unb.ca", role = c("cre", "cph")))
Description: Accurate estimates of the diets of predators are required in many areas of ecology, but for many species current methods are imprecise, limited to the last meal, and often biased. The diversity of fatty acids and their patterns in organisms, coupled with the narrow limitations on their biosynthesis, properties of digestion in monogastric animals, and the prevalence of large storage reservoirs of lipid in many predators, led us to propose the use of quantitative fatty acid signature analysis (QFASA) to study predator diets.
Depends: R (>= 3.2)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: Rsolnp, grid
RoxygenNote: 5.0.1
VignetteBuilder: rmarkdown, knitr
Suggests: knitr, rmarkdown, testthat, plyr, gtools
NeedsCompilation: no
Packaged: 2016-05-27 13:12:00 UTC; ec2-user
Author: Sara Iverson [aut], Chris Field [aut], Don Bowen [aut], Wade Blanchard [aut], Connie Stewart [aut, cph], Shelly Lang [aut], Justin Kamerman [cre, cph]
Maintainer: Justin Kamerman <justin.kamerman@unb.ca>
Repository: CRAN
Date/Publication: 2016-05-27 15:46:28

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New package jose with initial version 0.1
Package: jose
Type: Package
Title: Javascript Object Signing and Encryption
Version: 0.1
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Description: A collection of specifications to securely transfer claims such as authorization information between parties. A JSON Web Token (JWT) contains claims used by systems to apply access control rules to its resources. One potential use case of the JWT is authentication and authorization for a system that exposes resources through OAuth 2.0.
License: MIT + file LICENSE
URL: https://datatracker.ietf.org/wg/jose/documents/ https://github.com/jeroenooms/jose
BugReports: https://github.com/jeroenooms/jose/issues
Depends: openssl (>= 0.9.4)
Imports: jsonlite
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Suggests: testthat, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2016-05-27 11:33:37 UTC; jeroen
Repository: CRAN
Date/Publication: 2016-05-27 15:50:53

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New package elpatron with initial version 0.0.1
Package: elpatron
Title: Bicycling Data Analysis with R
Version: 0.0.1
Authors@R: person("Jordan", "Mackie", email = "jmackie@protonmail.com", role = c("aut", "cre"))
Description: Functions to facilitate cycling analysis within the R environment.
Depends: R (>= 3.2.5)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, dplyr, purrr, lazyeval
Suggests: readr, raster, magrittr
URL: https://github.com/jmackie4/elpatron
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-25 16:01:41 UTC; jmach
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Repository: CRAN
Date/Publication: 2016-05-27 15:58:48

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Package Compositional updated to version 1.3 with previous version 1.2 dated 2016-04-01

Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 1.2 dated 2016-04-01 and 1.3 dated 2016-05-27

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Package SpatPCA updated to version 1.1.1.1 with previous version 1.1.1.0 dated 2016-02-11

Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>

Diff between SpatPCA versions 1.1.1.0 dated 2016-02-11 and 1.1.1.1 dated 2016-05-27

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 SpatPCA-1.1.1.1/SpatPCA/man/SpatPCA-package.Rd |    6 +--
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Package PoisBinOrdNonNor updated to version 1.1 with previous version 1.0 dated 2015-05-17

Title: Generation of Up to Four Different Types of Variables
Description: Generation of a chosen number of count, binary, ordinal, and continuous (via Fleishman polynomials) random variables, with specified correlations and marginal properties.
Author: Hakan Demirtas, Rachel Nordgren, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>

Diff between PoisBinOrdNonNor versions 1.0 dated 2015-05-17 and 1.1 dated 2016-05-27

 DESCRIPTION                     |   16 +--
 MD5                             |   10 -
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New package GK2011 with initial version 0.1.3
Package: GK2011
Type: Package
Title: Gaines and Kuklinski (2011) Estimators for Hybrid Experiments
Version: 0.1.3
Date: 2016-05-26
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com"))
Description: Implementations of the treatment effect estimators for hybrid (self-selection) experiments, as developed by Brian J. Gaines and James H. Kuklinski, (2011), "Experimental Estimation of Heterogeneous Treatment Effects Related to Self-Selection," American Journal of Political Science 55(3): 724-736.
License: GPL (>= 2)
URL: https://github.com/leeper/GK2011
BugReports: https://github.com/leeper/GK2011/issues
LazyData: TRUE
Imports: stats
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 16:42:11 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-27 10:59:07

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Thu, 26 May 2016

Package texmexseq updated to version 0.2 with previous version 0.1 dated 2015-03-11

Title: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>

Diff between texmexseq versions 0.1 dated 2015-03-11 and 0.2 dated 2016-05-26

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Package spfrontier updated to version 0.2.3 with previous version 0.1.12 dated 2014-12-21

Title: Spatial Stochastic Frontier Models
Description: A set of tools for estimation of various spatial specifications of stochastic frontier models.
Author: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>
Maintainer: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>

Diff between spfrontier versions 0.1.12 dated 2014-12-21 and 0.2.3 dated 2016-05-26

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Package PST updated to version 0.88 with previous version 0.86 dated 2015-02-18

Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho <alexis.gabadinho@unige.ch>

Diff between PST versions 0.86 dated 2015-02-18 and 0.88 dated 2016-05-26

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Package HTSCluster updated to version 2.0.8 with previous version 2.0.4 dated 2014-08-26

Title: Clustering High-Throughput Transcriptome Sequencing (HTS) Data
Description: A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis- Rabusseau
Maintainer: Andrea Rau <andrea.rau@jouy.inra.fr>

Diff between HTSCluster versions 2.0.4 dated 2014-08-26 and 2.0.8 dated 2016-05-26

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Package DiversityOccupancy updated to version 1.0.4 with previous version 1.0.3 dated 2016-05-12

Title: Building Diversity Models from Multiple Species Occupancy Models
Description: Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Author: Derek Corcoran [aut, cre], Dylan Kesler [aut], Nicole Michel [ctb], Mike Meredith [ctb]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>

Diff between DiversityOccupancy versions 1.0.3 dated 2016-05-12 and 1.0.4 dated 2016-05-26

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New package CHFF with initial version 0.1.0
Package: CHFF
Type: Package
Title: Closest History Flow Field Forecasting for Bivariate Time Series
Version: 0.1.0
Author: Patrick Fleming
Maintainer: Kyle A. Caudle <kyle.caudle@sdsmt.edu>
Description: The software matches the current history to the closest history in a time series to build a forecast.
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-05-26 17:06:11 UTC; kcaudle
Repository: CRAN
Date/Publication: 2016-05-26 23:10:00

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New package BetaBit with initial version 1.2.1
Package: BetaBit
Title: Mini Games from Adventures of Beta and Bit
Version: 1.2.1
Authors@R: c( person("Przemysław", "Biecek", email = "przemyslaw.biecek@gmail.com", role = c("aut", "cre")), person("Witold", "Chodor", email = "witoldchodor@gmail.com", role = c("trl")), person("Katarzyna", "Fak", role = c("aut")), person("Foundation", "SmarterPoland.pl", email = "smarterpoland@gmail.com", role = c("cph")))
Description: Two games: proton and frequon. Both are console-based data-crunching games for younger and older data scientists. Act as a data-hacker and find Slawomir Pietraszko's credentials to the Proton server. You have to solve four data-based puzzles to find the login and password. There are many ways to solve these puzzles. You may use loops, data filtering, ordering, aggregation or other tools. Only basics knowledge of R is required to play the game, yet the more functions you know, the more approaches you can try. The knowledge of 'dplyr' package is not required but may be very helpful. This game is linked with the ,,Pietraszko's Cave'' story available at <http://biecek.pl/BetaBit/Warsaw>. It's a part of Beta and Bit series. You will find more about the Beta and Bit series at <http://betabit.wiki>.
Depends: R (>= 3.0.0)
Imports: digest
License: GPL-2
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 17:14:41 UTC; pbiecek
Author: Przemysław Biecek [aut, cre], Witold Chodor [trl], Katarzyna Fak [aut], Foundation SmarterPoland.pl [cph]
Maintainer: Przemysław Biecek <przemyslaw.biecek@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 23:09:59

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Package vcfR updated to version 1.1.0 with previous version 1.0.0 dated 2016-02-22

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

Diff between vcfR versions 1.0.0 dated 2016-02-22 and 1.1.0 dated 2016-05-26

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Package unfoldr updated to version 0.5.5 with previous version 0.5.1 dated 2016-05-04

Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in the estimation of the joint size-shape-orientation distribution of spheroidal shaped particles based on the same measured quantities of corresponding planar section profiles. A single trivariate discretized version of the (stereological) integral equation in the case of prolate and oblate spheroids is solved numerically by the EM algorithm. The estimation of diameter distribution of spheres from planar sections (Wicksell's corpuscle problem) is also implemented. Further, the package provides routines for the simulation of a Poisson germ- grain process with either spheroids, spherocylinders or spheres as grains together with functions for planar sections. For the purpose of exact simulation a bivariate size-shape distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

Diff between unfoldr versions 0.5.1 dated 2016-05-04 and 0.5.5 dated 2016-05-26

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Package Qtools updated to version 1.1 with previous version 1.0 dated 2016-02-04

Title: Utilities for Quantiles
Description: This is a collection of functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, and restricted quantile regression.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>

Diff between Qtools versions 1.0 dated 2016-02-04 and 1.1 dated 2016-05-26

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Package rfoaas updated to version 0.1.9 with previous version 0.1.8 dated 2015-10-24

Title: R Interface to 'FOAAS'
Description: R access to the 'FOAAS' (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between rfoaas versions 0.1.8 dated 2015-10-24 and 0.1.9 dated 2016-05-26

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Package inctools updated to version 1.0.5 with previous version 1.0.3 dated 2016-05-18

Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross- sectional surveys and for calibrating tests for recent infection.
Author: Alex Welte [aut], Eduard Grebe [cre, aut], Avery McIntosh [aut], Petra Bäumler [aut], Reshma Kassanjee [ctb], Hilmarie Brand [ctb], Cari Van Schalkwyk [ctb], Yuruo Li [ctb], Simon Daniel [ctb], Stefano Ongarello [ctb], Yusuke Asai [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>

Diff between inctools versions 1.0.3 dated 2016-05-18 and 1.0.5 dated 2016-05-26

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Package imputeMulti updated to version 0.4.6 with previous version 0.4.5 dated 2016-05-05

Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

Diff between imputeMulti versions 0.4.5 dated 2016-05-05 and 0.4.6 dated 2016-05-26

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New package heatmaply with initial version 0.3.2
Package: heatmaply
Type: Package
Title: Interactive Heat Maps Using 'plotly'
Version: 0.3.2
Date: 2016-05-25
Authors@R: c(person("Tal", "Galili", role = c("aut", "cre", "cph"), email = "tal.galili@gmail.com", comment = "http://www.r-statistics.com"))
Description: Create interactive heatmaps that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms. Heatmaps are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive heatmaps allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the heatmap by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar heatmaps as 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), and the ability to zoom from the dendrogram panes.
Depends: R (>= 3.0.0), plotly (>= 3.6.0), viridis
Imports: ggplot2, dendextend, magrittr (>= 1.0.1), reshape2, scales, utils, stats
Suggests: knitr, rmarkdown, gplots
VignetteBuilder: knitr
License: GPL-2 | GPL-3
URL: https://cran.r-project.org/package=heatmaply, https://github.com/talgalili/heatmaply/, http://www.r-statistics.com/tag/heatmaply/
BugReports: https://github.com/talgalili/heatmaply/issues
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 07:40:04 UTC; junior
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com)
Maintainer: Tal Galili <tal.galili@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 17:50:25

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Package Haplin updated to version 6.0.1 with previous version 6.0 dated 2016-05-25

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>

Diff between Haplin versions 6.0 dated 2016-05-25 and 6.0.1 dated 2016-05-26

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Package ecospat updated to version 2.0 with previous version 1.1 dated 2015-03-06

Title: Spatial Ecology Miscellaneous Methods
Description: Colection of R functions and data sets for the support of spatial ecology analyses with a focus on pre-, core and post- modelling analyses of species distribution, niche quantification and community assembly., written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann [aut], Valeria Di Cola [cre, aut], Blaise Petitpierre [ctb], Frank Breiner [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb], Robin Engler [ctb], Wim Hordijk [ctb], Julien Pottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb], Dorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis [ctb], Daniel Scherrer [ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte Ndiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb], Antoine Guisan [aut]
Maintainer: Valeria Di Cola <valeria.dicola@unil.ch>

Diff between ecospat versions 1.1 dated 2015-03-06 and 2.0 dated 2016-05-26

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New package fakeR with initial version 1.0
Package: fakeR
Type: Package
Title: Simulates Data from a Data Frame of Different Variable Types
Version: 1.0
Date: 2016-05-25
Authors@R: c(person("Lily", "Zhang", email = "lilyhzhang1029@gmail.com", role = c("aut", "cre")), person("Dustin","Tingley", email = "dtingley@gov.harvard.edu", role = c("aut")))
Description: Generates fake data from a dataset of different variable types. The package contains the functions simulate_dataset and simulate_dataset_ts to simulate time-independent and time-dependent data. It randomly samples character and factor variables from contingency tables and numeric and ordered factors from a multivariate normal distribution. It currently supports the simulation of stationary and zero-inflated count time series.
License: CC0
Imports: mvtnorm, polycor, pscl, VGAM, stats
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-26 06:59:29 UTC; lilyzhang
Author: Lily Zhang [aut, cre], Dustin Tingley [aut]
Maintainer: Lily Zhang <lilyhzhang1029@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 17:54:23

More information about fakeR at CRAN
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Package ddst updated to version 1.4 with previous version 1.03 dated 2012-08-19

Title: Data Driven Smooth Tests
Description: Smooth testing of goodness of fit. These tests are data driven (alternative hypothesis is dynamically selected based on data). In this package you will find various tests for exponent, Gaussian, Gumbel and uniform distribution.
Author: Przemyslaw Biecek (R code), Teresa Ledwina (support, descriptions)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between ddst versions 1.03 dated 2012-08-19 and 1.4 dated 2016-05-26

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Package climtrends updated to version 1.0.6 with previous version 1.0.5 dated 2015-09-20

Title: Statistical Methods for Climate Sciences
Description: Absolute homogeneity tests SNHT absolute 1-breaks, 1-break, SD different from 1, 2-breaks, Buishand, Pettitt, von Neumann ratio and ratio-rank, Worsley, and Craddock, Relative homogeneity tests SNHT absolute 1-breaks, 1-break SD different from 1, 2-breaks, Peterson and Easterling, and Vincent, Differences in scale between two groups Siegel–Tukey, Create reference time series mean, weights/correlation, finding outliers Grubbs, ESD, MAD, Tietjen Moore, Hampel, etc.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>

Diff between climtrends versions 1.0.5 dated 2015-09-20 and 1.0.6 dated 2016-05-26

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Package AnalyzeTS updated to version 1.9 with previous version 1.8 dated 2016-04-04

Title: Analyze Time Series
Description: Main function of package is helped to analyze time series, peculiar is fuzzy time series. The package can calculate AIC value of common time series models and propose the best models according AIC values. To fuzzy time series by "Chen", "Sing", "Heuristic" and "Chen-Hsu" models, also can fuzzy and forecast time series by Abbasov-Mamedova model.
Author: Tran Thi Ngoc Han <tranthingochan01011994@gmail.com>_ Doan Hai Nghi <Hainghi1426262609121094@gmail.com> _ Mai Thi Hong Diem <maidiemks@gmail.com> _ Nguyen Thi Diem My <myntdhg@gmail.com> _ Hong Viet Minh <hongvietminh@gmail.com> _ Vo Van Tai <vvtai@ctu.edu.vn>
Maintainer: Hong Viet Minh <hongvietminh@gmail.com>

Diff between AnalyzeTS versions 1.8 dated 2016-04-04 and 1.9 dated 2016-05-26

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Package intcox (with last version 0.9.3) was removed from CRAN

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

2013-02-25 0.9.3

Permanent link
Package replicationInterval updated to version 2.0.1 with previous version 1.0.0 dated 2015-07-07

Title: Replication Interval Functions
Description: A common problem faced by journal reviewers and authors is the question of whether the results of a replication study are consistent with the original published study. One solution to this problem is to examine the effect size from the original study and generate the range of effect sizes that could reasonably be obtained (due to random sampling) in a replication attempt (i.e., calculate a replication interval). If a replication effect size falls outside the replication interval, then that effect likely did not occur due to the effects of sampling error alone. Alternatively, if a replication effect size falls within the replication interval, then the replication effect could have reasonably occurred due to the effects of sampling error alone. This package has functions that calculate the replication interval for the correlation (i.e., r), standardized mean difference (i.e., d-value), and mean. The calculations used in version 2.0.0 and onward differ from past calculations due to feedback during the journal review process. The new calculations allow for a more precise interpretation of the replication interval.
Author: David Stanley
Maintainer: David Stanley <dstanley@uoguelph.ca>

Diff between replicationInterval versions 1.0.0 dated 2015-07-07 and 2.0.1 dated 2016-05-26

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Package GSODR updated to version 0.1.6 with previous version 0.1.5 dated 2016-05-16

Title: Download, Clean and Generate New Variables from GSOD Data
Description: Download, clean, reformat and create new variables from the USA National Climatic Data Center (NCDC) Global Surface Summary of the Day (GSOD) weather stations data, <https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod>. The function, get_GSOD(), retrieves data from the GSOD ftp site and reformats it from United States Customary System (USCS) units to International System of Units (SI), also for convenience elevation is converted from decimetres to metres. Stations are individually checked for number of missing days, as defined by the user, to assure data quality. Stations with too many missing observations are omitted from final file. Stations with missing latitude or longitude or values for both of 0 are omitted. Also omitted are stations with a latitude of < -90 or > 90 or longitude of < - 180 or > 180. Output is returned as a comma-separated values (CSV) file written to disk in a location selected by the user, which summarises each year by station and includes new variables: actual vapor pressure, saturation vapor pressure and relative humidity are calculated from the original GSOD data. The resulting files can be as large as 500mb depending on the user's stringency for missing data and geographic area of interest. Be sure to have sufficient RAM and disk space as well as a reasonably fast internet connection to use this package to perform this operation. However, for much smaller and more manageable data sets, an individual country of interest may be selected as well as only stations falling between -60/60 degrees latitude for agroclimatology work or individual stations if the station ID is known. The resulting files include station data (e.g., station name, country, latitude, longitude, elevation) for use in a geographic information system (GIS). The function was largely based on T. Hengl's 'getGSOD.R' script, available from <http://spatial-analyst.net/book/system/files/getGSOD.R> with enhancements to be more cross-platform, faster and more flexible. See the GSOD readme.txt <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre], Tomislav Hengl [ctb], Andy Nelson [ctb], Kay Sumfleth [ctb]
Maintainer: Adam Sparks <adamhsparks@gmail.com>

Diff between GSODR versions 0.1.5 dated 2016-05-16 and 0.1.6 dated 2016-05-26

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Package forecTheta updated to version 2.2 with previous version 2.1 dated 2016-03-07

Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models. Contains several cross-validation routines.
Author: Jose Augusto Fiorucci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>

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Package elliptic updated to version 1.3-7 with previous version 1.3-5 dated 2014-11-05

Title: Elliptic Functions
Description: A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between elliptic versions 1.3-5 dated 2014-11-05 and 1.3-7 dated 2016-05-26

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Package Davies updated to version 1.1-9 with previous version 1.1-8 dated 2012-11-07

Title: The Davies Quantile Function
Description: Various utilities for the Davies distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between Davies versions 1.1-8 dated 2012-11-07 and 1.1-9 dated 2016-05-26

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Package contfrac updated to version 1.1-10 with previous version 1.1-9 dated 2013-01-21

Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between contfrac versions 1.1-9 dated 2013-01-21 and 1.1-10 dated 2016-05-26

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Wed, 25 May 2016

Package popprxl updated to version 0.1.2 with previous version 0.1.1 dated 2015-11-24

Title: Read GenAlEx Files Directly from Excel
Description: GenAlEx is a popular Excel macro for genetic analysis. The 'poppr' R package allows import of GenAlEx formatted CSV data. This package serves as a small 'poppr' add on for those who have trouble or simply do not want to export their data into CSV format.
Author: Zhian N. Kamvar [cre, aut], Niklaus J. Grünwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>

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Package openssl updated to version 0.9.4 with previous version 0.9.3 dated 2016-05-04

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut], Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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Package treescape updated to version 1.9.16 with previous version 1.8.16 dated 2016-04-01

Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treescapeServer()'.
Author: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>

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New package mvtboost with initial version 0.5.0
Package: mvtboost
Type: Package
Title: Tree Boosting for Multivariate Outcomes
Version: 0.5.0
Date: 2016-05-25
Author: Patrick Miller [aut, cre]
Maintainer: Patrick Miller <patrick.mil10@gmail.com>
Description: Fits a multivariate model of decision trees for multiple, continuous outcome variables. A model for each outcome variable is fit separately, selecting predictors that explain covariance in the outcomes. Built on top of 'gbm', which fits an ensemble of decision trees to univariate outcomes.
License: GPL (>= 2) | file LICENSE
URL: https://github.com/patr1ckm/mvtboost
BugReports: https://github.com/patr1ckm/mvtboost/issues
Depends: R (>= 3.0.0)
Suggests: testthat, plyr, MASS, parallel, lars, ggplot2, knitr, rmarkdown
Imports: gbm, RColorBrewer, stats, graphics, grDevices, utils,
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-25 14:41:06 UTC; pmille13
Repository: CRAN
Date/Publication: 2016-05-25 18:08:26

More information about mvtboost at CRAN
Permanent link

Package matlabr updated to version 1.1.3 with previous version 1.1 dated 2015-10-21

Title: An Interface for MATLAB using System Calls
Description: Provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to 'R.matlab', which creates a MATLAB server.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package fslr updated to version 1.6.4.0 with previous version 1.5.0 dated 2015-10-21

Title: Wrapper Functions for FSL (FMRIB Software Library) from Functional MRI of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL (http:// fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used neuroimaging software, using system commands. The goal is to be able to interface with FSL completely in R, where you pass R objects of class "nifti", implemented by package 'oro.nifti', and the function executes an FSL command and returns an R object of class "nifti" if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package blackbox updated to version 1.0.8 with previous version 1.0 dated 2016-04-14

Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph], Leblois Raphaël [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between blackbox versions 1.0 dated 2016-04-14 and 1.0.8 dated 2016-05-25

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Package Rlabkey updated to version 2.1.130 with previous version 2.1.129 dated 2015-12-15

Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

Diff between Rlabkey versions 2.1.129 dated 2015-12-15 and 2.1.130 dated 2016-05-25

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Package mlt.docreg updated to version 0.0-32 with previous version 0.0-30 dated 2016-02-24

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

Diff between mlt.docreg versions 0.0-30 dated 2016-02-24 and 0.0-32 dated 2016-05-25

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Package mlt updated to version 0.0-33 with previous version 0.0-32 dated 2016-05-25

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt versions 0.0-32 dated 2016-05-25 and 0.0-33 dated 2016-05-25

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More information about mlt at CRAN
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Package mcPAFit updated to version 0.1.3 with previous version 0.1.2 dated 2016-05-17

Title: Estimating Preferential Attachment from a Single Network Snapshot by Markov Chain Monte Carlo
Description: A Markov chain Monte Carlo method is provided to estimate the preferential attachment function from a single network snapshot. Conventional methods require the complete information about the appearance order of all nodes and edges in the network. This package incorporates the appearance order into the state space and estimates it together with the preferential attachment function. Auxiliary variables are introduced to facilitate fast Gibbs sampling.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>

Diff between mcPAFit versions 0.1.2 dated 2016-05-17 and 0.1.3 dated 2016-05-25

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Package genie updated to version 1.0.2 with previous version 1.0.0 dated 2016-03-07

Title: A New, Fast, and Outlier Resistant Hierarchical Clustering Algorithm
Description: A new hierarchical clustering linkage criterion: the Genie algorithm links two clusters in such a way that a chosen economic inequity measure (e.g., the Gini index) of the cluster sizes does not increase drastically above a given threshold. Benchmarks indicate a high practical usefulness of the introduced method: it most often outperforms the Ward or average linkage in terms of the clustering quality while retaining the single linkage speed, see (Gagolewski et al. 2016 <DOI:10.1016/j.ins.2016.05.003>) for more details.
Author: Marek Gagolewski [aut, cre], Maciej Bartoszuk [aut], Anna Cena [aut]
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between genie versions 1.0.0 dated 2016-03-07 and 1.0.2 dated 2016-05-25

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Package BigVAR updated to version 1.0.1 with previous version 1.0 dated 2016-05-17

Title: Dimension Reduction Methods for Multivariate Time Series
Description: Estimates VAR and VARX models with structured Lasso Penalties.
Author: Will Nicholson [cre, aut], David Matteson [aut], Jacob Bien [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>

Diff between BigVAR versions 1.0 dated 2016-05-17 and 1.0.1 dated 2016-05-25

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Package SeqFeatR updated to version 0.2.3 with previous version 0.2.2 dated 2016-03-24

Title: A Tool to Associate FASTA Sequences and Features
Description: 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, or Bayes. 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 <bettina.budeus@stud.uni-due.de>

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Package Haplin updated to version 6.0 with previous version 5.5 dated 2015-05-15

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>

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Package kantorovich updated to version 2.0.0 with previous version 1.1.0 dated 2016-02-04

Title: Kantorovich Distance Between Probability Measures
Description: Computes the Kantorovich distance between two probability measures on a finite set.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>

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Package Directional updated to version 2.0 with previous version 1.9 dated 2016-04-21

Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

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New package condSURV with initial version 0.1.0
Package: condSURV
Type: Package
Title: Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data
Version: 0.1.0
Date: 2016-05-25
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Luis Meira-Machado <lmachado@math.uminho.pt>
Description: Method to implement some newly developed methods for the estimation of the conditional survival function.
Depends: R (>= 3.0.1)
License: GPL (>= 2)
LazyData: TRUE
Imports: KernSmooth, doParallel, parallel, doRNG, foreach
NeedsCompilation: yes
Packaged: 2016-05-25 09:43:25 UTC; Sestelo
Repository: CRAN
Date/Publication: 2016-05-25 11:56:42

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Package mlt updated to version 0.0-32 with previous version 0.0-30 dated 2016-02-20

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package treethresh updated to version 0.1-9 with previous version 0.1-8 dated 2014-11-20

Title: Methods for Tree-Based Local Adaptive Thresholding
Description: An implementation of TreeThresh, a locally adaptive version of EbayesThresh.
Author: Ludger Evers <ludger.evers@glasgow.ac.uk> and Tim Heaton <t.heaton@sheffield.ac.uk>
Maintainer: Ludger Evers <ludger.evers@glasgow.ac.uk>

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Package simcausal updated to version 0.5.1 with previous version 0.5.0 dated 2016-02-20

Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using structural equations, with emphasis on problems in causal inference. Specify interventions and simulate from intervened data generating distributions. Define and evaluate treatment-specific means, the average treatment effects and coefficients from working marginal structural models. User interface designed to facilitate the conduct of transparent and reproducible simulation studies, and allows concise expression of complex functional dependencies for a large number of time-varying nodes. See the package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre], Mark J. van der Laan [aut], Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>

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 simcausal-0.5.1/simcausal/man/sparseAdjMat.to.igraph.Rd          |    2 
 simcausal-0.5.1/simcausal/man/vecfun.add.Rd                      |    2 
 simcausal-0.5.1/simcausal/man/vecfun.all.print.Rd                |    2 
 simcausal-0.5.1/simcausal/man/vecfun.print.Rd                    |    2 
 simcausal-0.5.1/simcausal/man/vecfun.remove.Rd                   |    2 
 simcausal-0.5.1/simcausal/man/vecfun.reset.Rd                    |    2 
 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_00.R           |  872 +++++-----
 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_01_nets.R      |    9 
 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_02_MV.R        |   38 
 simcausal-0.5.1/simcausal/tests/examples/MSM.examples.R          |only
 simcausal-0.5.1/simcausal/tests/examples/add.action.R            |   30 
 simcausal-0.5.1/simcausal/tests/examples/example.simnets.R       |   17 
 simcausal-0.5.1/simcausal/tests/examples/set.DAG.R               |  238 +-
 simcausal-0.5.1/simcausal/tests/examples/set.targetE.examples.R  |only
 simcausal-0.5.1/simcausal/tests/examples/sim.impute.examples12.R |    2 
 simcausal-0.5.1/simcausal/vignettes/SimCausal_Networks_2016.bib  |only
 simcausal-0.5.1/simcausal/vignettes/mystyles.sty                 |only
 simcausal-0.5.1/simcausal/vignettes/psi.n.mat.rda                |only
 simcausal-0.5.1/simcausal/vignettes/simcausal_vignette.Rnw       |  592 +++---
 83 files changed, 2392 insertions(+), 2217 deletions(-)

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