Thu, 01 Nov 2018

Package rstpm2 updated to version 1.4.4 with previous version 1.4.2 dated 2018-05-29

Title: Generalized Survival Models
Description: R implementation of generalized survival models (GSMs) and smooth accelerated failure time (AFT) models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x).
Author: Mark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb], Lasse Hjort Jakobsen [ctb], Alessandro Gasparini [ctb], Gordon Smyth [cph], Patrick Alken [cph], Simon Wood [cph], Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>

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Package RNiftyReg updated to version 2.6.4 with previous version 2.6.1 dated 2017-11-26

Title: Image Registration Using the 'NiftyReg' Library
Description: Provides an 'R' interface to the 'NiftyReg' image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden [cre, aut], Marc Modat [aut], Benoit Presles [aut], Thanasis Anthopoulos [aut], Pankaj Daga [aut]
Maintainer: Jon Clayden <code@clayden.org>

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Package polymapR updated to version 1.0.18 with previous version 1.0.17 dated 2018-08-24

Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>.
Author: Peter Bourke [aut, cre], Geert van Geest [aut]
Maintainer: Peter Bourke <pbourkey@gmail.com>

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Package kohonen updated to version 3.0.7 with previous version 3.0.6 dated 2018-08-17

Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>

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Package RNeXML updated to version 2.2.0 with previous version 2.1.2 dated 2018-08-13

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>), Kseniia Shumelchyk [aut], Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package pkgnet updated to version 0.2.1 with previous version 0.2.0 dated 2018-04-30

Title: Get Network Representation of an R Package
Description: Tools from the domain of graph theory can be used to quantify the complexity and vulnerability to failure of a software package. That is the guiding philosophy of this package. 'pkgnet' provides tools to analyze the dependencies between functions in an R package and between its imported packages.
Author: Brian Burns [aut, cre], James Lamb [aut], Patrick Boueri [ctb], Jay Qi [ctb]
Maintainer: Brian Burns <brian.burns@uptake.com>

Diff between pkgnet versions 0.2.0 dated 2018-04-30 and 0.2.1 dated 2018-11-01

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Package ggiraph updated to version 0.6.0 with previous version 0.5.0 dated 2018-09-27

Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre], Mike Bostock [cph] (d3.js), Speros Kokenes [cph] (d3-lasso), Eric Shull [cph] (saveSvgAsPng js library), Eric Book [ctb] (hline and vline geoms)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package carfima updated to version 2.0.0 with previous version 1.0.0 dated 2017-10-23

Title: Continuous-Time Fractionally Integrated ARMA Process for Irregularly Spaced Long-Memory Time Series Data
Description: We provide a toolbox to fit a continuous-time fractionally integrated ARMA process (CARFIMA) on univariate and irregularly spaced time series data via frequentist or Bayesian machinery. A general-order CARFIMA(p, H, q) model for p>q is specified in Tsai and Chan (2005) <doi:10.1111/j.1467-9868.2005.00522.x> and it involves (p+q+2) unknown model parameters, i.e., p AR parameters, q MA parameters, Hurst parameter H, and process uncertainty (standard deviation) sigma. The package produces their maximum likelihood estimates and asymptotic uncertainties using a global optimizer called the differential evolution algorithm. It also produces their posterior distributions via Metropolis within a Gibbs sampler equipped with adaptive Markov chain Monte Carlo for posterior sampling. These fitting procedures, however, may produce numerical errors if p>2. The toolbox also contains a function to simulate discrete time series data from CARFIMA(p, H, q) process given the model parameters and observation times.
Author: Hyungsuk Tak [aut] (<https://orcid.org/0000-0003-0334-8742>), Henghsiu Tsai [aut], Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>

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Package shotGroups updated to version 0.7.4 with previous version 0.7.3 dated 2017-01-18

Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape, precision, and accuracy. This includes graphical methods, descriptive statistics, and inference tests using standard, but also non-parametric and robust statistical methods. Implements distributions for radial error in bivariate normal variables. Works with files exported by 'OnTarget PC/TDS', 'Silver Mountain' e-target, 'ShotMarker' e-target, or 'Taran', as well as with custom data files in text format. Supports inference from range statistics like extreme spread. Includes a set of web-based graphical user interfaces.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>

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Package quanteda updated to version 1.3.13 with previous version 1.3.4 dated 2018-07-15

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and ngrams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph] (<https://orcid.org/0000-0002-0797-564X>), Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>), Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>), Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>), Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>), Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>), Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>), Patrick O. Perry [aut] (<https://orcid.org/0000-0001-7460-127X>), Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>), Benjamin Lauderdale [aut] (<https://orcid.org/0000-0003-3090-0969>), William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>), Christian Müller [ctb], Lori Young [dtc] (Lexicoder Sentiment Dictionary 2015), Stuart Soroka [dtc] (Lexicoder Sentiment Dictionary 2015), Ian Fellows [cph] (authored wordcloud C source code (modified)), European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package NetworkToolbox updated to version 1.2.2 with previous version 1.2.1 dated 2018-09-19

Title: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>

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Package ftsa updated to version 5.2 with previous version 5.1 dated 2018-10-07

Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>

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Package RcppAnnoy updated to version 0.0.11 with previous version 0.0.10 dated 2017-09-25

Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package Matrix updated to version 1.2-15 with previous version 1.2-14 dated 2018-04-09

Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse and with pattern, logical and numeric entries. Numerous methods for and operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Author: Douglas Bates [aut], Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Timothy A. Davis [ctb] (SuiteSparse and 'cs' C libraries, notably CHOLMOD, AMD; collaborators listed in dir(pattern = '^[A-Z]+[.]txt$', full.names=TRUE, system.file('doc', 'SuiteSparse', package='Matrix'))), Jens Oehlschlägel [ctb] (initial nearPD()), Jason Riedy [ctb] (condest() and onenormest() for octave, Copyright: Regents of the University of California), R Core Team [ctb] (base R matrix implementation)
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>

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Package cgraph updated to version 3.0.0 with previous version 2.0.3 dated 2018-09-24

Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various functions including basic arithmetic, trigonometry functions, and linear algebra functions. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>

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Package arfima updated to version 1.7-0 with previous version 1.6-8 dated 2018-09-27

Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time series, possibly mixed with ARMA, regression, transfer-function components. Exact methods (MLE, forecasting, simulation) are used. Bug reports should be done via GitHub (at <https://github.com/JQVeenstra/arfima>), where the development version of this package lives; it can be installed using devtools.
Author: JQ (Justin) Veenstra [aut, cre], A.I. McLeod [aut]
Maintainer: JQ Veenstra <jqveenstra@gmail.com>

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Package hei (with last version 0.1.0) was removed from CRAN

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

2017-08-17 0.1.0

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Package rSARP (with last version 1.0.0) was removed from CRAN

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

2016-05-25 1.0.0

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Package MM2Sdata (with last version 1.0.1) was removed from CRAN

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

2015-06-16 1.0.1
2015-06-13 1.0.0

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Package checkr updated to version 0.4.0 with previous version 0.3.0 dated 2018-06-27

Title: Check the Properties of Common R Objects
Description: Expressive, assertive, pipe-friendly functions to check the properties of common R objects. In the case of failure the functions issue informative error messages.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package hazer updated to version 1.1.1 with previous version 1.0.1 dated 2018-05-02

Title: Identifying Foggy and Cloudy Images by Quantifying Haziness
Description: Provides a set of functions to estimate haziness of an image based on RGB bands. It returns a haze factor, varying from 0 to 1, a metric for fogginess and cloudiness. The package also presents additional functions to estimate brightness, darkness and contrast rasters of the RGB image. This package can be used for several applications such as inference of weather quality data and performing environmental studies from interpreting digital images.
Author: Bijan Seyednasrollah
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>

Diff between hazer versions 1.0.1 dated 2018-05-02 and 1.1.1 dated 2018-11-01

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Package polyglot updated to version 0.2.1 with previous version 0.1.1 dated 2018-03-19

Title: Learn Foreign Language Vocabulary
Description: Use the R console as an interactive learning environment to memorize any two columns dataset.
Author: Félix Luginbuhl [aut, cre]
Maintainer: Félix Luginbuhl <felix.luginbuhl@protonmail.ch>

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Package MASS updated to version 7.3-51.1 with previous version 7.3-51 dated 2018-10-16

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package incidence updated to version 1.5.0 with previous version 1.4.1 dated 2018-08-24

Title: Compute, Handle, Plot and Model Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut], Zhian N. Kamvar [aut, cre], Rich FitzJohn [aut], Jun Cai [ctb], Sangeeta Bhatia [ctb], Jakob Schumacher [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

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More information about incidence at CRAN
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Package hutils updated to version 1.3.0 with previous version 1.2.0 dated 2018-08-20

Title: Miscellaneous R Functions and Aliases
Description: Provides utility functions for, and drawing on, the 'data.table' package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of 'utils' and the author.
Author: Hugh Parsonage [aut, cre], Michael Frasco [ctb], Ben Hamner [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

Diff between hutils versions 1.2.0 dated 2018-08-20 and 1.3.0 dated 2018-11-01

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Package mleap updated to version 0.1.3 with previous version 0.1.2 dated 2018-05-23

Title: Interface to 'MLeap'
Description: A 'sparklyr' <https://spark.rstudio.com> extension that provides an interface to 'MLeap' <https://github.com/combust/mleap>, an open source library that enables exporting and serving of 'Apache Spark' pipelines.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>

Diff between mleap versions 0.1.2 dated 2018-05-23 and 0.1.3 dated 2018-11-01

 DESCRIPTION                        |    6 +++---
 MD5                                |   12 ++++++------
 NEWS.md                            |    4 ++++
 R/dependencies.R                   |    8 +++++++-
 R/installers.R                     |    6 +++---
 inst/extdata/config.json           |    4 ++--
 tests/testthat/test-installation.R |    2 +-
 7 files changed, 26 insertions(+), 16 deletions(-)

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Package ballr updated to version 0.2.3 with previous version 0.2.2 dated 2018-10-19

Title: Access to Current and Historical Basketball Data
Description: Provides simple functions for accessing data/tables on <http://www.basketball-reference.com>.
Author: Ryan Elmore [cre, aut], Peter DeWitt [ctb]
Maintainer: Ryan Elmore <rtelmore@gmail.com>

Diff between ballr versions 0.2.2 dated 2018-10-19 and 0.2.3 dated 2018-11-01

 DESCRIPTION                           |    6 +++---
 MD5                                   |   32 ++++++++++++++++----------------
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 inst/doc/use-ballr.html               |    6 +++---
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 17 files changed, 53 insertions(+), 23 deletions(-)

More information about ballr at CRAN
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Package maGUI (with last version 2.2) was removed from CRAN

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

2017-03-04 2.2
2017-02-16 2.1
2017-01-11 2.0
2015-10-12 1.0

Permanent link
Package HBP (with last version 0.1.2) was removed from CRAN

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

2017-07-08 0.1.2

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