Wed, 14 Nov 2018

Package giphyr updated to version 0.1.3 with previous version 0.1.2 dated 2017-10-21

Title: R Interface to the Giphy API
Description: An interface to the 'API' of 'Giphy', a popular index-based search engine for 'GIFs' and animated stickers (see <http://giphy.com/faq> and <https://github.com/Giphy/GiphyAPI> for more information about 'Giphy' and its 'API') . This package also provides a 'RStudio Addin', which can help users easily search and download 'GIFs' and insert them to a 'rmarkdown' presentation.
Author: Hao Zhu [aut, cre] (<https://orcid.org/0000-0002-3386-6076>)
Maintainer: Hao Zhu <haozhu233@gmail.com>

Diff between giphyr versions 0.1.2 dated 2017-10-21 and 0.1.3 dated 2018-11-14

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More information about giphyr at CRAN
Permanent link

Package echarts4r updated to version 0.2.0 with previous version 0.1.1 dated 2018-09-17

Title: Create Interactive Graphs with 'Echarts JavaScript' Version 4
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 34 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>

Diff between echarts4r versions 0.1.1 dated 2018-09-17 and 0.2.0 dated 2018-11-14

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More information about echarts4r at CRAN
Permanent link

Package bReeze updated to version 0.4-3 with previous version 0.4-2 dated 2018-01-05

Title: Functions for Wind Resource Assessment
Description: A collection of functions to analyse, visualize and interpret wind data and to calculate the potential energy production of wind turbines.
Author: Christian Graul and Carsten Poppinga
Maintainer: Christian Graul <christian.graul@gmail.com>

Diff between bReeze versions 0.4-2 dated 2018-01-05 and 0.4-3 dated 2018-11-14

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Package RJafroc updated to version 1.1.0 with previous version 1.0.2 dated 2018-05-31

Title: Modeling, Analysis, Validation and Visualization of Observer Performance Studies in Diagnostic Radiology
Description: Tools for quantitative assessment of medical imaging systems, radiologists or computer aided ('CAD') algorithms. Implements methods described in a book: 'Chakraborty' 'DP' (2017), "Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples", Taylor-Francis <https://www.crcpress.com/9781482214840> and its Online Appendices <https://github.com/dpc10ster/onlinebookk21778>. Data collection paradigms include receiver operating characteristic ('ROC') and a location specific extension, namely free-response 'ROC' ('FROC'). 'ROC' data consists of a single rating per image, where the rating is the perceived confidence level the image is of a diseased patient. 'FROC' data consists of a variable number (including zero) of mark-rating pairs per image, where a mark is the location of a clinically reportable suspicious region and the rating is the corresponding confidence level that it is a true lesion. The software supersedes the current Windows version of 'JAFROC' software <http://www.devchakraborty.com> which is no longer supported. 'RJafroc' is derived from it being an enhanced R version of original Windows 'JAFROC'. Implemented are a number of figures of merit quantifying performance, functions for visualizing operating characteristics; three ROC ratings data curve-fitting algorithms: the 'binormal' model ('BM'), the contaminated binormal model ('CBM') and the radiological search model ('RSM'). Also implemented is maximum likelihood fitting of paired ROC data utilizing the correlated 'CBM' model ('CORCBM'). Unlike the 'BM', 'CBM', 'CORCBM' and the 'RSM' predict proper ROC curves that do not cross the chance diagonal or display inappropriate hooks, usually near the upper right corner of the plots. 'RSM' fitting yields measures of search and lesion-classification performances, in addition to the usual case-classification performance measured by the area under the 'ROC' curve. Search performance is the ability to find lesions while avoiding finding non-lesions. Lesion-classification performance is the ability to discriminate between found lesions and non-lesions. For fully crossed study designs, termed multiple-reader multiple-case, significance testing of reader-averaged figure-of-merit differences between modalities is implemented via both 'Dorfman', 'Berbaum' and 'Metz' ('DBM') and the 'Obuchowski' and 'Rockette' ('OR') methods, both substantially improved by 'Hillis'. Single treatment analysis allows comparison of performance of a group of radiologists to a specified value, or comparison of 'CAD' performance to a group of radiologists interpreting the same cases. Sample size estimation tools are provided for 'ROC' studies that allow estimation of relevant variances from a pilot study to predict required numbers of readers and cases in a pivotal study. 'FROC' sample size estimation is implemented in Online Appendix Chapter 19 available at <https://github.com/dpc10ster/onlinebookk21778>. Utility and data file manipulation functions allow data to be read in any of the currently used input formats, including Excel, and the results of the analysis can be viewed in text or Excel output files.
Author: Dev Chakraborty [cre, aut, cph], Xuetong Zhai [aut], Lucy D'Agostino McGowan [ctb], Alejandro RodriguezRuiz [ctb]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>

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Package BDgraph updated to version 2.53 with previous version 2.52 dated 2018-10-03

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi et al. (2017) <doi:10.1111/rssc.12171>, and Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>, Ernst Wit [aut], Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

Diff between BDgraph versions 2.52 dated 2018-10-03 and 2.53 dated 2018-11-14

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New package tableschema.r with initial version 1.1.0
Package: tableschema.r
Type: Package
Title: Frictionless Data Table Schema
Version: 1.1.0
Date: 2018-11-5
Authors@R: c(person("Kleanthis", "Koupidis", email = "koupidis@okfn.gr", role = c("aut", "cre")), person("Lazaros", "Ioannidis", email = "larjohn@gmail.com", role = "aut"), person("Charalampos", "Bratsas", email = "cbratsas@math.auth.gr", role = "aut"), person("Open Knowledge International", email = "info@okfn.org", role = "cph"))
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>
Description: Allows to work with 'Table Schema' (<http://specs.frictionlessdata.io/table-schema/>). 'Table Schema' is well suited for use cases around handling and validating tabular data in text formats such as 'csv', but its utility extends well beyond this core usage, towards a range of applications where data benefits from a portable schema format. The 'tableschema.r' package can load and validate any table schema descriptor, allow the creation and modification of descriptors, expose methods for reading and streaming data that conforms to a 'Table Schema' via the 'Tabular Data Resource' abstraction.
URL: https://github.com/frictionlessdata/tableschema-r
BugReports: https://github.com/frictionlessdata/tableschema-r/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: config, future, httr, iterators, jsonlite, jsonvalidate, lubridate, purrr, R6, RCurl, rlist, stringr, urltools
Suggests: covr, foreach, testthat
Collate: 'constraints.checkUnique.R' 'constraints.checkRequired.R' 'constraints.checkPattern.R' 'constraints.checkMinLength.R' 'constraints.checkMinimum.R' 'constraints.checkMaxLength.R' 'constraints.checkMaximum.R' 'constraints.checkEnum.R' 'constraints.R' 'types.castArray.R' 'types.castYearmonth.R' 'types.castYear.R' 'types.castTime.R' 'types.castString.R' 'types.castObject.R' 'types.castNumber.R' 'types.castList.R' 'types.castInteger.R' 'types.castGeopoint.R' 'types.castGeojson.R' 'types.castDuration.R' 'types.castDatetime.R' 'types.castDate.R' 'types.castBoolean.R' 'types.castAny.R' 'types.R' 'field.R' 'helpers.R' 'infer.R' 'is.valid.R' 'tableschemaerror.R' 'profile.R' 'readable.R' 'readable.array.R' 'readable.connection.R' 'schema.R' 'table.R' 'tableschema.r.R' 'validate.R' 'writable.R'
RoxygenNote: 6.1.0.9000
NeedsCompilation: no
Packaged: 2018-11-14 15:09:47 UTC; akis_
Author: Kleanthis Koupidis [aut, cre], Lazaros Ioannidis [aut], Charalampos Bratsas [aut], Open Knowledge International [cph]
Repository: CRAN
Date/Publication: 2018-11-14 16:50:03 UTC

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New package mixsqp with initial version 0.1-79
Encoding: UTF-8
Type: Package
Package: mixsqp
Version: 0.1-79
Date: 2018-11-05
Title: Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
Authors@R: c(person("Youngseok","Kim",role="aut", email="youngseok@uchicago.edu"), person("Peter","Carbonetto",role=c("aut","cre"), email="peter.carbonetto@gmail.com"), person("Mihai","Anitescu",role="aut"), person("Matthew","Stephens",role="aut"))
URL: https://github.com/stephenslab/mixsqp
BugReports: https://github.com/stephenslab/mixsqp/issues
SystemRequirements: C++11
Depends: R (>= 3.3.0)
Description: Provides optimization algorithms based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithms are expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly in large data sets. The algorithms are described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2012) <arXiv:1806.01412>.
License: MIT + file LICENSE
Imports: stats, Rcpp (>= 0.12.15)
Suggests: Rmosek, REBayes, testthat, knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
LazyData: true
NeedsCompilation: yes
VignetteBuilder: knitr
RoxygenNote: 6.1.0.9000
Packaged: 2018-11-05 22:41:03 UTC; pcarbo
Author: Youngseok Kim [aut], Peter Carbonetto [aut, cre], Mihai Anitescu [aut], Matthew Stephens [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-14 15:10:03 UTC

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New package sparklyr.nested with initial version 0.0.3
Package: sparklyr.nested
Title: A 'sparklyr' Extension for Nested Data
Version: 0.0.3
Authors@R: c( person("Matt", "Pollock", email = "mpollock@mitre.org", role = c("aut", "cre")), person(family = "The MITRE Corporation", role = c("cph")) )
Maintainer: Matt Pollock <mpollock@mitre.org>
Description: A 'sparklyr' extension adding the capability to work easily with nested data.
Depends: R (>= 3.3)
Imports: sparklyr, jsonlite, listviewer, dplyr, rlang, purrr
License: Apache License 2.0 | file LICENSE
SystemRequirements: Spark: 1.6.x or 2.x
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: testthat
BugReports: https://github.com/mitre/sparklyr.nested/issues
NeedsCompilation: no
Packaged: 2018-11-05 14:33:31 UTC; mpollock
Author: Matt Pollock [aut, cre], The MITRE Corporation [cph]
Repository: CRAN
Date/Publication: 2018-11-14 14:40:03 UTC

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New package sensmediation with initial version 0.2.0
Package: sensmediation
Title: Parametric Estimation and Sensitivity Analysis of Direct and Indirect Effects
Version: 0.2.0
Date: 2018-11-05
Author: Anita Lindmark <anita.lindmark@umu.se>
Maintainer: Anita Lindmark <anita.lindmark@umu.se>
Description: We implement functions to estimate and perform sensitivity analysis to unobserved confounding of direct and indirect effects introduced in Lindmark, de Luna and Eriksson (2018) <doi:10.1002/sim.7620>. The estimation and sensitivity analysis are parametric, based on probit and/or linear regression models. Sensitivity analysis is implemented for unobserved confounding of the exposure-mediator, mediator-outcome and exposure-outcome relationships.
Depends: R (>= 3.5.0)
Imports: maxLik (>= 1.3-4), mvtnorm (>= 1.0-8), stats (>= 3.5.1)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Collate: 'calc.effects.R' 'coefs.sensmed.R' 'mediationmethods.R' 'sensmediation.R'
NeedsCompilation: no
Packaged: 2018-11-05 10:16:26 UTC; anli0053
Repository: CRAN
Date/Publication: 2018-11-14 14:40:08 UTC

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New package RGenData with initial version 1.0
Package: RGenData
Type: Package
Title: Generates Multivariate Nonnormal Data and Determines How Many Factors to Retain
Version: 1.0
Author: John Ruscio
Maintainer: John Ruscio <ruscio@tcnj.edu>
Description: The GenDataSample() and GenDataPopulation() functions create, respectively, a sample or population of multivariate nonnormal data using methods described in Ruscio and Kaczetow (2008). Both of these functions call a FactorAnalysis() function to reproduce a correlation matrix. The EFACompData() function allows users to determine how many factors to retain in an exploratory factor analysis of an empirical data set using a method described in Ruscio and Roche (2012). The latter function uses populations of comparison data created by calling the GenDataPopulation() function. <DOI: 10.1080/00273170802285693>. <DOI: 10.1037/a0025697>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-05 17:02:12 UTC; oliviaortelli
Repository: CRAN
Date/Publication: 2018-11-14 15:00:09 UTC

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New package pluscode with initial version 0.1.0
Package: pluscode
Type: Package
Title: Encoder for Google 'Pluscodes'
Version: 0.1.0
Author: Michael Doyle
Maintainer: Michael Doyle <michaeledoyle7@gmail.com>
Description: Retrieves a 'pluscode' by inputting latitude and longitude. Includes additional functions to retrieve neighbouring 'pluscodes'.
License: GPL-2
LazyData: FALSE
Imports: httr, jsonlite
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2018-11-05 14:01:37 UTC; michael.doyle@paddypowerbetfair.com
Repository: CRAN
Date/Publication: 2018-11-14 15:00:03 UTC

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New package majesticR with initial version 0.1.0
Package: majesticR
Type: Package
Title: R Interface to Access the 'Majestic' API
Version: 0.1.0
Authors@R: person("Remi", "Bacha", email = "hello@remibacha.com", role = c("aut", "cre"))
Description: Implements methods for querying backlink data from 'Majestic' using its API (<https://developer-support.majestic.com/api/>). 'Majestic' API uses a basic authentication with an API key.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: utils, jsonlite
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-05 11:37:00 UTC; rbacha
Author: Remi Bacha [aut, cre]
Maintainer: Remi Bacha <hello@remibacha.com>
Repository: CRAN
Date/Publication: 2018-11-14 15:00:06 UTC

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Package LNIRT updated to version 0.3.5 with previous version 0.3.0 dated 2018-03-24

Title: LogNormal Response Time Item Response Theory Models
Description: Allows the simultaneous analysis of responses and response times in an Item Response Theory (IRT) modelling framework. Supports covariates for item and person (random) parameters. Parameter estimation is done with a MCMC algorithm. LNIRT replaces the package CIRT, which was written by Rinke Klein Entink. For reference, see the paper by Fox, Klein Entink and Van der Linden (2007), "Modeling of Responses and Response Times with the Package cirt", Journal of Statistical Software, <doi:10.18637/jss.v020.i07>.
Author: Jean-Paul Fox, Konrad Klotzke, Rinke Klein Entink
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>

Diff between LNIRT versions 0.3.0 dated 2018-03-24 and 0.3.5 dated 2018-11-14

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 R/summary.R |    4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

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Package GPM updated to version 2.0.0 with previous version 1.0.2 dated 2018-07-23

Title: Gaussian Process Modeling of Multi-Response Datasets
Description: A general and efficient package for modeling (possibly noisy) datasets via Gaussian processes.
Author: Ramin Bostanabad, Wei Chen (IDEAL)
Maintainer: Ramin Bostanabad <bostanabad@u.northwestern.edu>

Diff between GPM versions 1.0.2 dated 2018-07-23 and 2.0.0 dated 2018-11-14

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 GPM-2.0.0/GPM/NAMESPACE            |    6 
 GPM-2.0.0/GPM/R/Draw.R             |   47 +++----
 GPM-2.0.0/GPM/R/Fit.R              |  244 +++++++++++++++----------------------
 GPM-2.0.0/GPM/R/NLogL.R            |   43 +++---
 GPM-2.0.0/GPM/R/Predict.R          |   73 +++++------
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 GPM-2.0.0/GPM/man/Draw.Rd          |    6 
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New package GB2group with initial version 0.1.0
Package: GB2group
Type: Package
Title: Estimation of the Generalised Beta Distribution of the Second Kind from Grouped Data
Version: 0.1.0
Author: Vanesa Jorda <jordav@unican.es>, Jose Maria Sarabia <jose.sarabia@unican.es>, Markus Jäntti <markus.jantti@sofi.su.se>.
Maintainer: Vanesa Jorda <jordav@unican.es>
Depends: R (>= 3.1.0)
Imports: GB2, minpack.lm, ineq, numDeriv
Description: Estimation of the generalized beta distribution of the second kind (GB2) and related models using grouped data in form of income shares. The GB2 family is a general class of distributions that provides an accurate fit to income data. 'GB2group' includes functions to estimate the GB2, the Singh-Maddala, the Dagum, the Beta 2, the Lognormal and the Fisk distributions. 'GB2group' deploys two different econometric strategies to estimate these parametric distributions, non-linear least squares (NLS) and the generalised method of moments (GMM). Asymptotic standard errors are reported for the GMM estimates. Standard errors of the NLS estimates are obtained by Monte Carlo simulation. See Jorda et al. (2018) <arXiv:1808.09831> for a detailed description of the estimation procedure.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2018-11-05 16:27:59 UTC; Vanesa
Repository: CRAN
Date/Publication: 2018-11-14 15:00:15 UTC

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New package BondValuation with initial version 0.1.0
Package: BondValuation
Title: Fixed Coupon Bond Valuation Allowing for Odd Coupon Periods and Various Day Count Conventions
Date: 2018-11-05
Version: 0.1.0
Authors@R: person("Djatschenko","Wadim",email="wadim.djatschenko@gmx.de",role = c("aut", "cre"))
Description: Analysis of large datasets of fixed coupon bonds, allowing for irregular first and last coupon periods and various day count conventions. With this package you can compute the yield to maturity, the modified and MacAulay durations and the convexity of fixed-rate bonds. It provides the function AnnivDates, which can be used to evaluate the quality of the data and return time-invariant properties and temporal structure of a bond.
Depends: R (>= 2.15.1)
Imports: Rcpp, timeDate
LazyData: TRUE
License: GPL-3
RoxygenNote: 6.1.0
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2018-11-05 19:51:21 UTC; Wadim
Author: Djatschenko Wadim [aut, cre]
Maintainer: Djatschenko Wadim <wadim.djatschenko@gmx.de>
Repository: CRAN
Date/Publication: 2018-11-14 15:00:18 UTC

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New package adamethods with initial version 1.0
Package: adamethods
Type: Package
Title: Archetypoid Algorithms and Anomaly Detection
Version: 1.0
Date: 2018-11-05
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Description: Collection of several algorithms to obtain archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also allow to detect anomalies (outliers).
License: GPL (>= 2)
URL: https://www.R-project.org, https://www.uv.es/vivigui
Depends: R (>= 3.4.0)
Imports: Anthropometry, archetypes, FNN, foreach, nnls, parallel, reticulate, stats, tolerance, univOutl
Suggests: doParallel, fda
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-05 13:23:10 UTC; guillevinue
Repository: CRAN
Date/Publication: 2018-11-14 14:40:12 UTC

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Package RJSONIO updated to version 1.3-1.1 with previous version 1.3-1 dated 2018-11-12

Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang [aut, cre] (<https://orcid.org/0000-0003-0159-1546>), Jonathan Wallace [aut] (aka ninja9578, author of included libjson sources)
Maintainer: ORPHANED

Diff between RJSONIO versions 1.3-1 dated 2018-11-12 and 1.3-1.1 dated 2018-11-14

 RJSONIO-1.3-1.1/RJSONIO/DESCRIPTION                          |   13 +-
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 RJSONIO-1.3-1.1/RJSONIO/src/libjson/Source/JSONMemoryPool.h  |    2 
 RJSONIO-1.3-1.1/RJSONIO/src/libjson/Source/JSONValidator.cpp |    4 
 RJSONIO-1.3-1.1/RJSONIO/src/libjson/Source/JSONWorker.cpp    |    8 -
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 29 files changed, 83 insertions(+), 68 deletions(-)

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Package personalized updated to version 0.2.2 with previous version 0.2.1 dated 2018-09-19

Title: Estimation and Validation Methods for Subgroup Identification and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup identification and personalized medicine / precision medicine under the general subgroup identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>. This package is intended for use for both randomized controlled trials and observational studies.
Author: Jared Huling [aut, cre] (<https://orcid.org/0000-0003-0670-4845>), Aaron Potvien [ctb], Alexandros Karatzoglou [cph], Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>

Diff between personalized versions 0.2.1 dated 2018-09-19 and 0.2.2 dated 2018-11-14

 DESCRIPTION                                     |   14 ++---
 MD5                                             |   11 ++--
 R/est_subgroup_effects.R                        |    3 -
 R/summarize_subgroups.R                         |   12 ++--
 inst/CITATION                                   |only
 inst/doc/usage_of_the_personalized_package.html |   66 +++++++++---------------
 man/print.Rd                                    |    7 +-
 7 files changed, 54 insertions(+), 59 deletions(-)

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Package sdcTable updated to version 0.25 with previous version 0.24 dated 2018-07-24

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>

Diff between sdcTable versions 0.24 dated 2018-07-24 and 0.25 dated 2018-11-14

 sdcTable-0.24/sdcTable/README.md                          |only
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 sdcTable-0.25/sdcTable/MD5                                |   24 
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 sdcTable-0.25/sdcTable/inst/doc/sdcTable.html             | 2679 --------------
 sdcTable-0.25/sdcTable/man/calc.problemInstance-method.Rd |    4 
 sdcTable-0.25/sdcTable/man/calc.simpleTriplet-method.Rd   |    3 
 sdcTable-0.25/sdcTable/man/changeCellStatus.Rd            |    3 
 sdcTable-0.25/sdcTable/man/createArgusInput.Rd            |    8 
 sdcTable-0.25/sdcTable/man/get.simpleTriplet-method.Rd    |    3 
 sdcTable-0.25/sdcTable/man/runArgusBatchFile.Rd           |    5 
 sdcTable-0.25/sdcTable/man/sdcProb2df.Rd                  |    3 
 sdcTable-0.25/sdcTable/man/set.problemInstance-method.Rd  |    4 
 14 files changed, 156 insertions(+), 2609 deletions(-)

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New package RCSF with initial version 1.0.1
Package: RCSF
Type: Package
Title: Airborne LiDAR Filtering Method Based on Cloth Simulation
Version: 1.0.1
Date: 2018-11-04
Authors@R: c( person("Jean-Romain", "Roussel", email = "jean-romain.roussel.1@ulaval.ca", role = c("aut", "cre", "cph")), person("Jianbo", "Qi", email = "jianboqi@gmail.com", role = c("aut", "cph")), person("Wuming", "Zhang", email = "", role = c("cph")), person("Peng", "Wan", email = "", role = c( "cph")), person("Hongtao", "Wang", email = "", role = c("cph")), person("State Key Laboratory of Remote Sensing Science, Institute of Remote Sensing Science and Engineering, Beijing Normal University", role = c("cph")))
Description: Cloth Simulation Filter (CSF) is an airborne LiDAR (Light Detection and Ranging) ground points filtering algorithm which is based on cloth simulation. It tries to simulate the interactions between the cloth nodes and the corresponding LiDAR points, the locations of the cloth nodes can be determined to generate an approximation of the ground surface.
Depends: R (>= 3.1.0)
Suggests: testthat
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-11-04 15:14:03 UTC; jr
Author: Jean-Romain Roussel [aut, cre, cph], Jianbo Qi [aut, cph], Wuming Zhang [cph], Peng Wan [cph], Hongtao Wang [cph], State Key Laboratory of Remote Sensing Science, Institute of Remote Sensing Science and Engineering, Beijing Normal University [cph]
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Repository: CRAN
Date/Publication: 2018-11-14 11:10:06 UTC

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New package mixggm with initial version 1.0
Package: mixggm
Version: 1.0
Date: 2018-11-02
Title: Mixtures of Gaussian Graphical Models
Description: Mixtures of Gaussian graphical models for model-based clustering with sparse covariance and concentration matrices. See Fop, Murphy, and Scrucca (2018) <doi:10.1007/s11222-018-9838-y>.
Authors@R: c(person("Michael", "Fop", role = c("aut", "cre"), email = "michael.fop@ucd.ie", comment = c(ORCID = "0000-0003-3936-2757")), person("Luca", "Scrucca", role = "ctb", comment = c(ORCID = "0000-0003-3826-0484")), person("Thomas Brendan", "Murphy", role = "ctb", comment = c(ORCID = "0000-0002-5668-7046")))
Maintainer: Michael Fop <michael.fop@ucd.ie>
Depends: R (>= 3.3)
Imports: foreach, GA (>= 3.1), mclust (>= 5.4), memoise, network, Rcpp
LinkingTo: Rcpp, RcppArmadillo
License: GPL (>= 2)
Repository: CRAN
URL: https://github.com/michaelfop/mixggm
BugReports: https://github.com/michaelfop/mixggm/issues
ByteCompile: true
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2018-11-14 10:48:05 UTC; michael
Author: Michael Fop [aut, cre] (<https://orcid.org/0000-0003-3936-2757>), Luca Scrucca [ctb] (<https://orcid.org/0000-0003-3826-0484>), Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>)
Date/Publication: 2018-11-14 11:20:02 UTC

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New package MarketMatching with initial version 1.1.1
Package: MarketMatching
Type: Package
Title: Market Matching and Causal Impact Inference
Version: 1.1.1
Date: 2018-11-04
Authors@R: person("Larsen", "Kim", email = "kblarsen4@gmail.com", role = c("aut", "cre"))
Description: For a given test market find the best control markets using time series matching and analyze the impact of an intervention. The intervention could be be a marketing event or some other local business tactic that is being tested. The workflow implemented in MarketMatching utilizes dynamic time warping (the dtw package) to do the matching and the CausalImpact package to analyze the causal impact. In fact, this package can be considered a "workflow wrapper" for those two packages.
Depends: R (>= 3.5.0)
License: GPL (>= 3)
Imports: data.table, ggplot2, dplyr, utils, iterators, doParallel, parallel, foreach, reshape2, CausalImpact, zoo, bsts, scales, dtw
LazyData: true
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-05 07:47:15 UTC; thirdlovechangethisname
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-14 11:10:09 UTC

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New package forestHES with initial version 1.0-1
Package: forestHES
Version: 1.0-1
Date: 2018-11-4
Type: Package
Title: Forest Health Evaluation System at the Forest Stand Level in China
Authors@R: c(person(given="Zongzheng",family="Chai", email="chaizz@126.com",role=c("aut", "cre")))
Author: Zongzheng Chai [aut, cre]
Maintainer: Zongzheng Chai <chaizz@126.com>
Depends: R (>= 3.4.0)
Description: Assessing forest ecosystem health is an effective way for forest resource management.The national forest health evaluation system at the forest stand level using analytic hierarchy process, has a high application value and practical significance. The package can effectively and easily realize the total assessment process, and help foresters to further assess and management forest resources.
License: GPL (>= 2)
LazyData: TRUE
NeedsCompilation: no
Packaged: 2018-11-05 06:22:26 UTC; jlzhang
Repository: CRAN
Date/Publication: 2018-11-14 11:10:03 UTC

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New package EpiSignalDetection with initial version 0.1.0
Package: EpiSignalDetection
Type: Package
Title: Signal Detection Analysis
Version: 0.1.0
Date: 2018-10-29
Authors@R: c( person( given = "Lore", family = "Merdrignac", role = c("aut", "ctr"), email = "l.merdrignac@epiconcept.fr", comment = "Author of the package and original code"), person( given = "Joana", family = "Gomes Dias", role = c("aut", "fnd", "cre"), email = "joana.gomes.dias@ecdc.europa.eu", comment = "Project manager and package maintainer"), person( given = "Esther", family = "Kissling", role = c("aut", "ctr"), email = "e.kissling@epiconcept.fr"), person( given = "Tommi", family = "Karki", role = c("aut", "fnd"), email = "tommi.karki@ecdc.europa.eu"), person( given = "Margot", family = "Einoder-Moreno", role = c("ctb", "fnd"), email = "margot.einoder-moreno@ecdc.europa.eu"))
Description: Exploring time series for signal detection. It is specifically designed to detect possible outbreaks using infectious disease surveillance data at the European Union / European Economic Area or country level. Automatic detection tools used are presented in the paper "Monitoring count time series in R: aberration detection in public health surveillance", by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. The package includes: - Signal Detection tool, an interactive 'shiny' application in which the user can import external data and perform basic signal detection analyses; - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. This report can also be stratified by population characteristics (see 'Population' variable). This project was funded by the European Centre for Disease Prevention and Control.
Depends: R (>= 3.4.0)
License: EUPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: shiny, dplyr, pander, DT, surveillance, ISOweek, ggplot2, graphics, utils, knitr (>= 1.20), rmarkdown
VignetteBuilder: knitr
URL: http://atlas.ecdc.europa.eu/public/index.aspx
NeedsCompilation: no
Packaged: 2018-11-05 11:02:59 UTC; LMC
Author: Lore Merdrignac [aut, ctr] (Author of the package and original code), Joana Gomes Dias [aut, fnd, cre] (Project manager and package maintainer), Esther Kissling [aut, ctr], Tommi Karki [aut, fnd], Margot Einoder-Moreno [ctb, fnd]
Maintainer: Joana Gomes Dias <joana.gomes.dias@ecdc.europa.eu>
Repository: CRAN
Date/Publication: 2018-11-14 11:10:12 UTC

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New package EpiReport with initial version 0.1.0
Package: EpiReport
Type: Package
Title: Epidemiological Report
Version: 0.1.0
Date: 2018-10-31
Authors@R: c( person( given = "Lore", family = "Merdrignac", role = c("aut", "ctr", "cre"), email = "l.merdrignac@epiconcept.fr", comment = "Author of the package and original code"), person( given = "Tommi", family = "Karki", role = c("aut", "fnd"), email = "tommi.karki@ecdc.europa.eu"), person( given = "Esther", family = "Kissling", role = c("aut", "ctr"), email = "e.kissling@epiconcept.fr"), person( given = "Joana", family = "Gomes Dias", role = c("aut", "fnd"), email = "joana.gomes.dias@ecdc.europa.eu", comment = "Project manager"))
Description: Drafting an epidemiological report in 'Microsoft Word' format for a given disease, similar to the Annual Epidemiological Reports published by the European Centre for Disease Prevention and Control. Through standalone functions, it is specifically designed to generate each disease specific output presented in these reports and includes: - Table with the distribution of cases by Member State over the last five years; - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, by month, over the past five years; - Trend plot with the trend and number of cases at the European Union / European Economic Area level, by month, over the past five years; - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level. Two types of datasets can be used: - The default dataset of salmonella 2012-2016 data; - Any dataset specified as described in the vignette.
Depends: R (>= 3.4.0)
License: EUPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: officer, flextable, zoo, png, dplyr, tidyr, ggplot2, extrafont, graphics, utils, knitr (>= 1.20), rmarkdown
VignetteBuilder: knitr
URL: https://ecdc.europa.eu/en/annual-epidemiological-reports
NeedsCompilation: no
Packaged: 2018-11-05 10:27:12 UTC; LMC
Author: Lore Merdrignac [aut, ctr, cre] (Author of the package and original code), Tommi Karki [aut, fnd], Esther Kissling [aut, ctr], Joana Gomes Dias [aut, fnd] (Project manager)
Maintainer: Lore Merdrignac <l.merdrignac@epiconcept.fr>
Repository: CRAN
Date/Publication: 2018-11-14 11:10:16 UTC

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New package AutoStepwiseGLM with initial version 0.2.0
Package: AutoStepwiseGLM
Type: Package
Title: Builds Stepwise GLMs via Train and Test Approach
Version: 0.2.0
Author: Aaron England <aaron.england24@gmail.com>
Maintainer: Aaron England <aaron.england24@gmail.com>
Description: Randomly splits data into testing and training sets. Then, uses stepwise selection to fit numerous multiple regression models on the training data, and tests them on the test data. Returned for each model are plots comparing model Akaike Information Criterion (AIC), Pearson correlation coefficient (r) between the predicted and actual values, Mean Absolute Error (MAE), and R-Squared among the models. Each model is ranked relative to the other models by the model evaluation metrics (i.e., AIC, r, MAE, and R-Squared) and the model with the best mean ranking among the model evaluation metrics is returned. Model evaluation metric weights for AIC, r, MAE, and R-Squared are taken in as arguments as aic_wt, r_wt, mae_wt, and r_squ_wt, respectively. They are equally weighted as default but may be adjusted relative to each other if the user prefers one or more metrics to the others, Field, A. (2013, ISBN:978-1-4462-4918-5).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Depends: caret, formula.tools
NeedsCompilation: no
Packaged: 2018-11-04 17:00:25 UTC; aengland
Repository: CRAN
Date/Publication: 2018-11-14 11:20:06 UTC

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New package zipR with initial version 0.1.0
Package: zipR
Title: Pythonic Zip() for R
Version: 0.1.0
Authors@R: person("Leslie", "Huang", email = "lesliehuang@nyu.edu", role = c("aut", "cre"))
Description: Implements Python-style zip for R. Is a more flexible version of cbind.
Depends: R (>= 2.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: knitr, rmarkdown, devtools
URL: https://github.com/leslie-huang/zipR
BugReports: https://github.com/leslie-huang/zipR/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-02 20:21:12 UTC; lesliehuang
Author: Leslie Huang [aut, cre]
Maintainer: Leslie Huang <lesliehuang@nyu.edu>
Repository: CRAN
Date/Publication: 2018-11-14 10:20:03 UTC

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New package vegperiod with initial version 0.2.5
Package: vegperiod
Version: 0.2.5
Title: Determine Thermal Vegetation Periods
Authors@R: person("Robert", "Nuske", role=c("aut", "cre"), email="robert.nuske@mailbox.org", comment=c(ORCID="0000-0001-9773-2061"))
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Depends: R (>= 2.15.0)
Imports: utils
Suggests: curl, testthat (>= 1.0.2)
Description: Collection of common methods to determine growing season length in a simple manner. Start and end dates of the vegetation periods are calculated solely based on daily mean temperatures and the day of the year.
URL: https://github.com/rnuske/vegperiod
BugReports: https://github.com/rnuske/vegperiod/issues
Encoding: UTF-8
License: GPL (>= 3)
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-02 19:20:40 UTC; rnuske
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>)
Repository: CRAN
Date/Publication: 2018-11-14 10:20:06 UTC

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New package SolveRationalMatrixEquation with initial version 0.1.0
Package: SolveRationalMatrixEquation
Type: Package
Title: Solve Rational Matrix Equation
Version: 0.1.0
Author: Aditi Tiwari
Maintainer: Aditi Tiwari <aditi.jec31@gmail.com>
Description: Given a symmetric positive definite matrix Q and a non-singular matrix L, find symmetric positive definite solution X such that X = Q + L (X inv) L^T. Reference: Benner, P., Faßbender, H. On the Solution of the Rational Matrix Equation. Benner, Faßbender (2007) <doi:10.1155/2007/21850>.
License: GPL-2
Encoding: UTF-8
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-04 04:00:45 UTC; apple
Repository: CRAN
Date/Publication: 2018-11-14 10:40:09 UTC

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New package smoothROCtime with initial version 0.1.0
Package: smoothROCtime
Type: Package
Title: Smooth Time-Dependent ROC Curve Estimation
Version: 0.1.0
Author: Susana Diaz-Coto <UO266718@uniovi.es>
Maintainer: Susana Diaz-Coto <UO266718@uniovi.es>
Imports: ks
Suggests: KMsurv,lattice, survival
Description: Computes smooth estimations for the Cumulative/Dynamic and Incident/Dynamic ROC curves, in presence of right censorship, based on the bivariate kernel density estimation of the joint distribution function of the Marker and Time-to-event variables.
License: GPL
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-03 02:20:09 UTC; SUSANA
Repository: CRAN
Date/Publication: 2018-11-14 10:40:03 UTC

More information about smoothROCtime at CRAN
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New package semdrw with initial version 0.1.0
Package: semdrw
Type: Package
Title: 'SEM Shiny'
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: Interactive 'shiny' application for working with Structural Equation Modelling technique. Runtime examples are provided in the package function as well as at <https://kartikeyab.shinyapps.io/semwebappk/> .
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.0.3)
Imports: shiny,shinyAce,lavaan,semPlot,dplyr,semTools,psych
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-04 19:11:55 UTC; KARTIKEYA
Repository: CRAN
Date/Publication: 2018-11-14 11:00:02 UTC

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Package RPyGeo updated to version 1.0.0 with previous version 0.9-3 dated 2012-08-23

Title: ArcGIS Geoprocessing via Python
Description: Provides access to ArcGIS geoprocessing tools by building an interface between R and the ArcPy Python side-package via the reticulate package.
Author: Alexander Brenning [aut, cre], Fabian Polakowski [aut], Marc Becker [aut], Jannes Muenchow [ctb] (<https://orcid.org/0000-0001-7834-4717>)
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>

Diff between RPyGeo versions 0.9-3 dated 2012-08-23 and 1.0.0 dated 2018-11-14

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 RPyGeo-1.0.0/RPyGeo/DESCRIPTION                             |   46 
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 37 files changed, 148 insertions(+), 593 deletions(-)

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New package portalr with initial version 0.1.4
Package: portalr
Title: Create Useful Summaries of the Portal Data
Version: 0.1.4
Authors@R: c(person(c("Glenda", "M."), "Yenni", role = c("aut", "cre"), email = "glenda@weecology.org", comment = c(ORCID = "0000-0001-6969-1848")), person("Hao", "Ye", role = c("aut"), comment = c(ORCID = "0000-0002-8630-1458")), person(c("Erica", "M."), "Christensen", role = c("aut"), comment = c(ORCID = "0000-0002-5635-2502")), person(c("Juniper", "L."), "Simonis", role = c("aut"), comment = c(ORCID = "0000-0001-9798-0460")), person(c("Ellen", "K."), "Bledsoe", role = c("aut"), comment = c(ORCID = "0000-0002-3629-7235")), person(c("Renata", "M."), "Diaz", role = c("aut"), comment = c(ORCID = "0000-0003-0803-4734")), person(c("Shawn", "D."), "Taylor", role = c("aut"), comment = c(ORCID = "0000-0002-6178-6903")), person(c("Ethan", "P,"), "White", role = c("ctb"), comment = c(ORCID = "0000-0001-6728-7745")), person(c("S.K.", "Morgan"), "Ernest", role = c("aut"), comment = c(ORCID = "0000-0002-6026-8530")))
Description: Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahua desert. The raw data files can be found at <https://github.com/weecology/portalData>.
License: MIT + file LICENSE
URL: https://github.com/weecology/portalr
BugReports: https://github.com/weecology/portalr/issues
LazyData: true
Depends: R (>= 3.2.3)
Imports: dplyr, ggplot2, tidyr, zoo, lubridate, magrittr, httr, rlang, forecast, lunar, jsonlite
Suggests: httptest, digest, tidyverse, cowplot, knitr, rmarkdown
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-02 23:31:12 UTC; GlendaYenni
Author: Glenda M. Yenni [aut, cre] (<https://orcid.org/0000-0001-6969-1848>), Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>), Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>), Juniper L. Simonis [aut] (<https://orcid.org/0000-0001-9798-0460>), Ellen K. Bledsoe [aut] (<https://orcid.org/0000-0002-3629-7235>), Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>), Shawn D. Taylor [aut] (<https://orcid.org/0000-0002-6178-6903>), Ethan P, White [ctb] (<https://orcid.org/0000-0001-6728-7745>), S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>)
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Repository: CRAN
Date/Publication: 2018-11-14 11:00:07 UTC

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Package mnreadR updated to version 2.1.1 with previous version 2.1.0 dated 2018-07-06

Title: MNREAD Parameters Estimation and Curve Plotting
Description: Allows to analyze the reading data obtained with the MNREAD Acuity Chart, a continuous-text reading acuity chart for normal and low vision. Provides the necessary functions to plot the MNREAD curve and estimate automatically the four MNREAD parameters: Maximum Reading Speed, Critical Print Size, Reading Acuity and Reading Accessibility Index. Parameters can be estimated either with the standard method or with a nonlinear mixed-effects (NLME) modeling. See Calabrese et al. 2018 for more details <doi.org/10.1167/18.1.8>.
Author: Aurélie Calabrèse [aut, cre], J. Steve Mansfield [aut], Gordon E. Legge [aut]
Maintainer: Aurélie Calabrèse <acalabre@umn.edu>

Diff between mnreadR versions 2.1.0 dated 2018-07-06 and 2.1.1 dated 2018-11-14

 DESCRIPTION          |    8 +++++---
 MD5                  |   12 ++++++------
 R/acc_index.R        |    7 ++++++-
 R/all_mnread_param.R |   11 ++++++++---
 R/nlme_curve.R       |   28 +++++++++++++++++++++++++++-
 inst/CITATION        |    4 ++--
 man/nlmeCurve.Rd     |   28 +++++++++++++++++++++++++++-
 7 files changed, 81 insertions(+), 17 deletions(-)

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Package gllvm updated to version 1.1.0 with previous version 1.0 dated 2018-07-30

Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>). Details for gllvm, see Hui et al. (2015) <doi:10.1111/2041-210X.12236> and (2017) <doi:10.1080/10618600.2016.1164708> and Niku et al. (2017) <doi:10.1007/s13253-017-0304-7>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>

Diff between gllvm versions 1.0 dated 2018-07-30 and 1.1.0 dated 2018-11-14

 DESCRIPTION                 |   10 
 MD5                         |   56 ++--
 NAMESPACE                   |    9 
 R/TMBtrait.R                |   53 +++-
 R/anova.gllvm.R             |   83 ++++---
 R/coef.gllvm.R              |    8 
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 R/confint.gllvm.R           |   54 ++--
 R/getResidualCor.gllvm.R    |   24 +-
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 man/logLik.gllvm.Rd         |    2 
 man/ordiplot.gllvm.Rd       |    8 
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 man/residuals.gllvm.Rd      |    8 
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 29 files changed, 1299 insertions(+), 700 deletions(-)

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New package gamlss.countKinf with initial version 3.5.1
Package: gamlss.countKinf
Type: Package
Title: Generating and Fitting K-Inflated 'discrete gamlss.family' Distributions
Version: 3.5.1
Author: Saeed Mohammadpour <\email{s.mohammadpour1111@gamlil.com}>, Mikis Stasinopoulos <\email{d.stasinopoulos@londonmet.ac.uk}>
Maintainer: Saeed Mohammadpour <s.mohammadpour1111@gmail.com>
Depends: R (>= 2.2.1), gamlss.dist, gamlss (>= 5.0-0), stats
Description: This is an add on package to 'GAMLSS'. The main purpose of this package is generating and fitting inflated distributions at any desired point (0, 1, 2, ...). The function gen.Kinf() generates K-inflated version of an existing discrete 'GAMLSS' family distribution.
License: GPL-2 | GPL-3
LazyData: True
URL: http://www.gamlss.org/
NeedsCompilation: no
Packaged: 2018-11-02 18:29:23 UTC; User
Repository: CRAN
Date/Publication: 2018-11-14 10:30:03 UTC

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New package flobr with initial version 0.1.0
Package: flobr
Title: Convert Files to and from Binary Objects (BLOBs)
Version: 0.1.0
Authors@R: person("Joe", "Thorley", email = "joe@poissonconsulting.ca", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7683-4592"))
Description: Converts files to and from flobs. A flob is a file that was read into binary in integer-mode as little endian, saved as the single element of a named list (where the name is the extension of the original file) and then serialized before being coerced into a blob. Flobs are useful for writing and reading files to and from databases.
URL: https://github.com/poissonconsulting/flobr
BugReports: https://github.com/poissonconsulting/flobr/issues
Depends: R (>= 3.3.0)
Imports: err, checkr, blob, tools
Suggests: covr, spelling, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Language: en-CA
NeedsCompilation: no
Packaged: 2018-11-02 22:41:43 UTC; joe
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-11-14 10:40:06 UTC

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New package cNORM with initial version 1.0.1
Package: cNORM
Type: Package
Title: Continuous Norming
Version: 1.0.1
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>), Alexandra Lenhard [aut], Sebastian Gary [ctb]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Date: 2018-10-24
Authors@R: c(person("Wolfgang", "Lenhard", role = c("cre","aut"), email="wolfgang.lenhard@uni-wuerzburg.de", comment=c(ORCID = "0000-0002-8184-6889")), person("Alexandra", "Lenhard", role=c("aut")), person("Sebastian", "Gary", role=c("ctb")))
Description: Conventional methods for producing standard scores in psychometrics or biometrics are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low confidence for assessing extreme scores. The continuous norming method introduced by A. Lenhard et al. (2016), <doi:10.1177/1073191116656437>, generates continuous test norm scores on the basis of the raw data from standardization samples, without requiring assumptions about the distribution of the raw data: Norm scores are directly established from raw data by modeling the latter ones as a function of both percentile scores and an explanatory variable (e.g., age). The method minimizes bias arising from sampling and measurement error, while handling marked deviations from normality, addressing bottom or ceiling effects and capturing almost all of the variance in the original norm data sample.
Depends: R (>= 3.1.0)
Imports: lattice (>= 0.20), leaps (>= 3.0.0), latticeExtra (>= 0.6)
Suggests: knitr, rmarkdown, shiny, shinycssloaders, foreign, readxl
License: AGPL-3
VignetteBuilder: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Repository: CRAN
Encoding: UTF-8
LazyData: true
URL: https://www.psychometrica.de/cNorm_en.html, https://github.com/WLenhard/cNORM
BugReports: https://github.com/WLenhard/cNORM/issues
Packaged: 2018-11-02 19:51:43 UTC; gbpa005
Date/Publication: 2018-11-14 10:20:10 UTC

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Package nneo (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:

2017-06-15 0.1.0

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New package solitude with initial version 0.1.0
Package: solitude
Type: Package
Title: An Implementation of Isolation Forest
Version: 0.1.0
Authors@R: person("Komala Sheshachala", "Srikanth", email = "sri.teach@gmail.com", role = c("aut", "cre"))
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
URL: https://github.com/talegari/solitude
BugReports: https://github.com/talegari/solitude/issues
Imports: ranger (>= 0.10.0), data.table (>= 1.11.4), igraph (>= 1.2.2)
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-02 04:02:53 UTC; srikanth
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-14 09:20:03 UTC

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New package rJST with initial version 1.0
Package: rJST
Type: Package
Title: Joint Sentiment Topic Modelling
Version: 1.0
Date: 2018-11-02
Authors@R: c(person(given='Max', family='Boiten',role=c('cre','aut'),email='max_boiten@live.nl'), person(given='Chenghua', family='Lin', role='cph'), person(given='Yulan', family='He', role='cph'))
Maintainer: Max Boiten <max_boiten@live.nl>
Description: Estimates the Joint Sentiment Topic model and its reversed variety, as described by Lin and He, 2009 <DOI:10.1145/1645953.1646003> and Lin, He, Everson and Ruger (2012) <DOI:10.1109/TKDE.2011.48>.
License: GPL-3
Imports: magrittr, quanteda, reshape2, Rcpp (>= 0.12.12), RcppProgress, SnowballC
Depends: methods
Suggests: knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Collate: 'RcppExports.R' 'dictionary.R' 'topNwords.R' 'jst_reversed.R' 'jst.R' 'get_parameter.R' 'rJST.R'
Encoding: UTF-8
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-11-02 14:52:44 UTC; max_b
Author: Max Boiten [cre, aut], Chenghua Lin [cph], Yulan He [cph]
Repository: CRAN
Date/Publication: 2018-11-14 09:10:03 UTC

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New package pkgverse with initial version 0.0.1
Package: pkgverse
Version: 0.0.1
Title: Build a Meta-Package Universe
Description: Build your own universe of packages similar to the 'tidyverse' package <https://tidyverse.org/> with this meta-package creator. Create a package-verse, or meta package, by supplying a custom name for the collection of packages and the vector of desired package names to include– and optionally supply a destination directory, an indicator of whether to keep the created package directory, and/or a vector of verbs implement via the 'usethis' <http://usethis.r-lib.org/> package.
Authors@R: person("Michael Wayne", "Kearney", , "kearneymw@missouri.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0730-4694"))
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.0.9000
Imports: devtools, usethis, utils
License: CC0
URL: https://pkgverse.mikewk.com
BugReports: https://github.com/mkearney/pkgverse/issues
NeedsCompilation: no
Packaged: 2018-11-02 01:16:21 UTC; mwk
Author: Michael Wayne Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael Wayne Kearney <kearneymw@missouri.edu>
Repository: CRAN
Date/Publication: 2018-11-14 09:10:06 UTC

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New package metsyn with initial version 0.1.2
Package: metsyn
Type: Package
Title: Interface with the Meteo France Synop Data API
Version: 0.1.2
Date: 2018-11-01
Authors@R: person("Paul", "Poncet", , "paulponcet@yahoo.fr", role = c("aut", "cre"))
Description: Provides an interface with the Meteo France Synop data API (see <https://donneespubliques.meteofrance.fr/?fond=produit&id_produit=90&id_rubrique=32> for more information). The Meteo France Synop data are made of meteorological data recorded every three hours on 62 French meteorological stations.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.1.3)
Imports: foreach, readr, stringr, tibble, utils
URL: https://github.com/paulponcet/metsyn
BugReports: https://github.com/paulponcet/metsyn/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-02 16:22:09 UTC; YL1101
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Repository: CRAN
Date/Publication: 2018-11-14 09:20:06 UTC

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Package esquisse updated to version 0.1.7 with previous version 0.1.6 dated 2018-10-26

Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' charts interactively with drag-and-drop to map your variables. You can quickly visualize your data accordingly to their type, export to 'PNG' or 'PowerPoint', and retrieve the code to reproduce the chart.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Ian Carroll [ctb] (Facets support)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between esquisse versions 0.1.6 dated 2018-10-26 and 0.1.7 dated 2018-11-14

 DESCRIPTION                          |    8 ++--
 MD5                                  |   24 ++++++------
 NAMESPACE                            |   11 +++++
 NEWS.md                              |    7 +++
 R/esquisserServer.R                  |    6 +--
 R/esquisserUI.R                      |   24 +++++++++++-
 R/ggplot_helpers.R                   |   35 +++++++++++++-----
 R/ggplot_to_ppt.R                    |   15 ++++---
 R/input-dragula.R                    |   20 ++++++++--
 R/module-chartControls.R             |   67 +++++++++++++++++++++--------------
 R/module-code.R                      |   12 ++++++
 R/module-filterData.R                |    1 
 inst/www/dragula/dragula-bindings.js |    2 -
 13 files changed, 163 insertions(+), 69 deletions(-)

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New package dlbayes with initial version 0.1.0
Package: dlbayes
Type: Package
Title: Use Dirichlet Laplace Prior to Solve Linear Regression Problem and Do Variable Selection
Version: 0.1.0
Author: Shijia Zhang; Meng Li
Maintainer: Shijia Zhang <zsj27@mail.ustc.edu.cn>
Description: The Dirichlet Laplace shrinkage prior in Bayesian linear regression and variable selection, featuring: utility functions in implementing Dirichlet-Laplace priors such as visualization; scalability in Bayesian linear regression; penalized credible regions for variable selection.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: GIGrvg, expm, glmnet, MASS, LaplacesDemon, stats, graphics
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-02 14:16:54 UTC; 75747
Repository: CRAN
Date/Publication: 2018-11-14 09:20:09 UTC

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Package DescToolsAddIns updated to version 1.1 with previous version 1.0 dated 2018-03-10

Title: Some Functions to be Used as Shortcuts in 'RStudio'
Description: 'RStudio' as of recently offers the option to define addins and assign shortcuts to them. This package contains addins for a few most frequently used functions in a data scientist's (at least mine) daily work (like str(), example(), plot(), head(), view(), Desc()). Most of these functions will use the current selection in the editor window and send the specific command to the console while instantly executing it. Assigning shortcuts to these addins will save you quite a few keystrokes.
Author: Andri Signorell
Maintainer: Andri Signorell <andri@signorell.net>

Diff between DescToolsAddIns versions 1.0 dated 2018-03-10 and 1.1 dated 2018-11-14

 DESCRIPTION             |    8 +--
 MD5                     |   12 ++---
 NAMESPACE               |    6 +-
 NEWS                    |   11 +++++
 R/AddIns.R              |  102 ++++++++++++++++++++++++++++++++++++++++++++----
 inst/rstudio/addins.dcf |   26 ++++++++++--
 man/DescToolsAddIns.Rd  |   20 +++++++--
 7 files changed, 156 insertions(+), 29 deletions(-)

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New package BaMORC with initial version 1.0
Package: BaMORC
Type: Package
Title: Bayesian Model Optimized Reference Correction Method for Assigned and Unassigned Protein NMR Spectra
Version: 1.0
Depends: R (>= 3.1.0)
Date: 2018-10-18
Authors@R: c( person("Xi", "Chen", email = "billchenxi@gmail.com", comment = c(ORCID="0000-0001-7094-6748"), role = c("aut", "cre")), person("Andrey", "Smelter", email = "andrey.smeltor@gmail.com", comment = c(ORCID="0000-0003-3056-9225"), role = "aut"), person("Hunter", "Moseley", email = "hunter.moseley@uky.edu", comment = c(ORCID="0000-0003-3995-5368"), role = "aut") )
Description: Provides reference correction for protein NMR spectra. Bayesian Model Optimized Reference Correction (BaMORC) is utilizing Bayesian probabilistic framework to perform protein NMR referencing correction, currently for alpha and beta carbon-13 chemical shifts, without any resonance assignment and/or three-dimensional protein structure. For more detailed explanation, please refer to the paper "Automatic 13C Chemical Shift Reference Correction for Unassigned Protein NMR Spectra" <https://rdcu.be/4ly5> (Journal of Biomolecular NMR, Aug 2018)" <doi:10.1007/s10858-018-0202-5>.
URL: https://github.com/MoseleyBioinformaticsLab/BaMORC
BugReports: https://github.com/MoseleyBioinformaticsLab/BaMORC/issues
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: data.table, tidyr, DEoptim, httr, docopt, stringr, jsonlite, readr, devtools, RBMRB, BMRBr
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-02 13:12:01 UTC; bill
Author: Xi Chen [aut, cre] (<https://orcid.org/0000-0001-7094-6748>), Andrey Smelter [aut] (<https://orcid.org/0000-0003-3056-9225>), Hunter Moseley [aut] (<https://orcid.org/0000-0003-3995-5368>)
Maintainer: Xi Chen <billchenxi@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-14 09:20:13 UTC

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Package StMoSim updated to version 3.1 with previous version 3.0 dated 2014-10-16

Title: Plots a QQ-Norm Plot with Several Gaussian Simulations
Description: Plots a QQ-Norm Plot with several Gaussian simulations.
Author: Matthias Salvisberg
Maintainer: Matthias Salvisberg <matthias.salvisberg@gmail.com>

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Package RBesT updated to version 1.3-5 with previous version 1.3-4 dated 2018-10-17

Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases).
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Beat Neuenschwander [ctb], Heinz Schmidli [ctb], Baldur Magnusson [ctb], Yue Li [ctb], Satrajit Roychoudhury [ctb], Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R, R/stanmodels.R, src/Makevars, src/Makevars.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

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Package packrat updated to version 0.5.0 with previous version 0.4.9-3 dated 2018-06-01

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: Manage the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>

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New package Modalclust with initial version 0.7
Package: Modalclust
Type: Package
Title: Hierarchical Modal Clustering
Version: 0.7
Date: 2018-11-11
Author: Surajit Ray and Yansong Cheng
Maintainer: Surajit Ray <surajit.ray@glasgow.ac.uk>
Description: Performs Modal Clustering (MAC) including Hierarchical Modal Clustering (HMAC) along with their parallel implementation (PHMAC) over several processors. These model-based non-parametric clustering techniques can extract clusters in very high dimensions with arbitrary density shapes. By default clustering is performed over several resolutions and the results are summarised as a hierarchical tree. Associated plot functions are also provided. There is a package vignette that provides many examples. This version adheres to CRAN policy of not spanning more than two child processes by default.
Depends: R (>= 2.14.0), mvtnorm, zoo, class
Suggests: parallel, MASS
License: GPL-2
Packaged: 2018-11-13 20:32:16 UTC; sray
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-11-14 08:20:03 UTC

More information about Modalclust at CRAN
Permanent link

Package LVGP updated to version 2.1.4 with previous version 2.1.3 dated 2018-07-31

Title: Latent Variable Gaussian Process Modeling with Qualitative and Quantitative Input Variables
Description: Fit response surfaces for datasets with latent-variable Gaussian process modeling, predict responses for new inputs, and plot latent variables locations in the latent space (only 1D or 2D). The input variables of the datasets can be quantitative, qualitative/categorical or mixed. The output variable of the datasets is a scalar (quantitative). The optimization of the likelihood function is done using a successive approximation/relaxation algorithm similar to another GP modeling package "GPM". The modeling method is published in "A Latent Variable Approach to Gaussian Process Modeling with Qualitative and Quantitative Factors" by Yichi Zhang, Siyu Tao, Wei Chen, and Daniel W. Apley (2018) <arXiv:1806.07504>. The package is developed in IDEAL of Northwestern University.
Author: Siyu Tao, Yichi Zhang
Maintainer: Siyu Tao <siyutao2020@u.northwestern.edu>

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Package JFE updated to version 1.3 with previous version 1.2 dated 2018-03-02

Title: A Menu-Driven GUI for Data Analysis of Just Finance and Econometrics
Description: Support the decision analysis of international assets selection and portfolio backtesting.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

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Package histry updated to version 0.2.4 with previous version 0.2.2 dated 2018-06-25

Title: Enhanced Command History Tracking for R Sessions and Dynamic Documents
Description: Automatically tracks and makes programmatically available code evaluation history in R sessions and dynamic documents.
Author: Gabriel Becker [aut, cre]
Maintainer: Gabriel Becker <gabembecker@gmail.com>

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Package GJRM updated to version 0.1-5 with previous version 0.1-4 dated 2017-12-13

Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>

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Package palm updated to version 1.1.2 with previous version 1.1.1 dated 2018-05-03

Title: Fitting Point Process Models via the Palm Likelihood
Description: Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008) <DOI:10.1002/bimj.200610339>, maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package is chiefly focused on Neyman-Scott point processes, but can also fit void processes. The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a clustered point process. As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys.
Author: Ben Stevenson <ben.stevenson@auckland.ac.nz>
Maintainer: Ben Stevenson <ben.stevenson@auckland.ac.nz>

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Package anytime updated to version 0.3.3 with previous version 0.3.2 dated 2018-11-06

Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor, or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package HMMcopula updated to version 1.0.2 with previous version 1.0.1 dated 2018-10-28

Title: Markov Regime Switching Copula Models Estimation and Goodness of Fit
Description: R functions to estimate and perform goodness of fit test for several Markov regime switching and mixture bivariate copula models. The goodness of fit test is based on a Cramer von Mises statistic and uses the Rosenblatt transform and parametric bootstrap to estimate the p-value. The estimation of the copula parameters are based on the pseudo-maximum likelihood method using pseudo-observations defined as normalized ranks.
Author: Mamadou Yamar Thioub <mamadou-yamar.thioub@hec.ca>, Bouchra Nasri <bouchra.nasri@mail.mcgill.ca>, Romanic Pieugueu <romanic.pieugueu@gerad.ca>, and Bruno Remillard <bruno.remillard@hec.ca>
Maintainer: Mamadou Yamar Thioub <mamadou-yamar.thioub@hec.ca>

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Tue, 13 Nov 2018

Package MIAmaxent updated to version 1.0.0 with previous version 0.4.0 dated 2017-02-14

Title: A Modular, Integrated Approach to Maximum Entropy Distribution Modeling
Description: Tools for training, selecting, and evaluating maximum entropy (and standard logistic regression) distribution models. This package provides tools for user-controlled transformation of explanatory variables, selection of variables by nested model comparison, and flexible model evaluation and projection. It follows principles based on the maximum- likelihood interpretation of maximum entropy modeling, and uses infinitely- weighted logistic regression for model fitting.
Author: Julien Vollering [aut, cre], Sabrina Mazzoni [aut], Rune Halvorsen [aut], Steven Phillips [cph]
Maintainer: Julien Vollering <julien.vollering@hvl.no>

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Package neonUtilities updated to version 1.0.1 with previous version 1.0.0 dated 2018-11-03

Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <http://data.neonscience.org> or through the NEON Data API (see <http://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Christine Laney <claney@battelleecology.org>, Claire Lunch <clunch@battelleecology.org>
Maintainer: Claire Lunch <clunch@battelleecology.org>

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Package dbscan updated to version 1.1-3 with previous version 1.1-2 dated 2018-05-18

Title: Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms HDBSCAN (hierarchical DBSCAN) and the LOF (local outlier factor) algorithm. The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph], Matthew Piekenbrock [aut, cph], Sunil Arya [ctb, cph], David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package skpr updated to version 0.57.0 with previous version 0.56.1 dated 2018-09-21

Title: Design of Experiments Suite: Generate and Evaluate Optimal Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre], George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

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Package configr updated to version 0.3.4 with previous version 0.3.3 dated 2018-06-22

Title: An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

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Package dimRed updated to version 0.2.2 with previous version 0.2.1 dated 2018-11-09

Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction techniques from R packages and a common interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>

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Package deming updated to version 1.4 with previous version 1.3 dated 2018-10-08

Title: Deming, Theil-Sen, Passing-Bablock and Total Least Squares Regression
Description: Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>

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Package drugCombo updated to version 1.0.3 with previous version 1.0.2 dated 2018-06-15

Title: Drug Interaction Modeling Based on Loewe Additivity Following Harbron's Approach
Description: Perform assessment of synergy/antagonism for drug combinations based on the Loewe additivity model, following Harbron's approach (Statistics in Medicine, 2010, <doi:10.1002/sim.3916>). The package allows flexible modeling of the drug interaction index and supports "2-stage" estimation in addition to "1-stage" estimation, including bootstrap-based confidence intervals. The method requires data on the monotherapy responses and the package accommodates both checkerboard and ray designs. Functions are available for graphical exploration of model goodness-of-fit and diagnostics, as well as for synergy/antagonism assessment in 2D and 3D.
Author: Maxim Nazarov, Nele Goeyvaerts, Chris Harbron (original article and code)
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>

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Package bioset updated to version 0.2.3 with previous version 0.2.2 dated 2018-04-17

Title: Convert a Matrix of Raw Values into Nice and Tidy Data
Description: Functions to help dealing with raw data from measurements, like reading and transforming raw values organized in matrices, calculating and converting concentrations and calculating precision of duplicates / triplicates / ... . It is compatible with and building on top of some 'tidyverse'-packages.
Author: Eike Christian Kühn [aut, cre]
Maintainer: Eike Christian Kühn <eike.kuehn@pixelwoelkchen.de>

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Package RaceID updated to version 0.1.2 with previous version 0.1.1 dated 2018-08-07

Title: Identification of Cell Types and Inference of Lineage Trees from Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>

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Package pgbart updated to version 0.6.15 with previous version 0.6.12 dated 2018-07-06

Title: Bayesian Additive Regression Trees Using Particle Gibbs Sampler and Gibbs/Metropolis-Hastings Sampler
Description: The Particle Gibbs sampler and Gibbs/Metropolis-Hastings sampler were implemented to fit Bayesian additive regression tree model. Construction of the model (training) and prediction for a new data set (testing) can be separated. Our reference papers are: Lakshminarayanan B, Roy D, Teh Y W. Particle Gibbs for Bayesian additive regression trees[C], Artificial Intelligence and Statistics. 2015: 553-561, <http://proceedings.mlr.press/v38/lakshminarayanan15.pdf> and Chipman, H., George, E., and McCulloch R. (2010) Bayesian Additive Regression Trees. The Annals of Applied Statistics, 4,1, 266-298, <doi:10.1214/09-aoas285>.
Author: Pingyu Wang [aut, cre], Dai Feng [aut], Yang Bai [aut], Qiuyue Shi [aut], Zhicheng Zhao [aut], Fei Su [aut], Hugh Chipman [aut], Robert McCulloch [aut]
Maintainer: Pingyu Wang <applewangpingyu@gmail.com>

Diff between pgbart versions 0.6.12 dated 2018-07-06 and 0.6.15 dated 2018-11-13

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Package FateID updated to version 0.1.5 with previous version 0.1.4 dated 2018-08-07

Title: Quantification of Fate Bias in Multipotent Progenitors
Description: Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>

Diff between FateID versions 0.1.4 dated 2018-08-07 and 0.1.5 dated 2018-11-13

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Package multimode updated to version 1.4 with previous version 1.3 dated 2018-06-13

Title: Mode Testing and Exploring
Description: Different examples and methods for testing (including different proposals described in Ameijeiras-Alonso et al., 2018 <DOI:10.1007/s11749-018-0611-5>) and exploring (including the mode tree, mode forest and SiZer) the number of modes using nonparametric techniques.
Author: Jose Ameijeiras-Alonso [aut,cre], Rosa M. Crujeiras [aut], Alberto Rodríguez-Casal [aut], The R Core Team 1996-2012 [ctb,cph] (C function 'BinDist2' obtained from package 'stats'), The R Foundation 2005 [ctb,cph] (C function 'BinDist2' obtained from package 'stats')
Maintainer: Jose Ameijeiras-Alonso <jose.ameijeirasalonso@kuleuven.be>

Diff between multimode versions 1.3 dated 2018-06-13 and 1.4 dated 2018-11-13

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Package DescTools updated to version 0.99.26 with previous version 0.99.25 dated 2018-08-14

Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Andreas Alfons, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Kamil Barton, Ben Bolker, Hans W. Borchers, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Romain Francois, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Soeren Hojsgaard, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Christopher Jackson, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Duncan Temple Lang, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Henric Nilsson, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Nathan Russell, Nick Sabbe, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Karline Soetaert, Werner A. Stahel, Alec Stephenson, Mark Stevenson, Matthias Templ, Terry Therneau, Yves Tille, Adrian Trapletti, Joshua Ulrich, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Hadley Wickham, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>

Diff between DescTools versions 0.99.25 dated 2018-08-14 and 0.99.26 dated 2018-11-13

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Package sys updated to version 2.1 with previous version 2.0 dated 2018-11-06

Title: Powerful and Reliable Tools for Running System Commands in R
Description: Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales. On Unix platforms the package also provides functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a sandboxing mechanism.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between sys versions 2.0 dated 2018-11-06 and 2.1 dated 2018-11-13

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Package Rmpi updated to version 0.6-9 with previous version 0.6-8 dated 2018-11-10

Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>

Diff between Rmpi versions 0.6-8 dated 2018-11-10 and 0.6-9 dated 2018-11-13

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Package helixvis updated to version 1.0.1 with previous version 0.9.1 dated 2018-06-25

Title: Visualize Alpha-Helical Peptide Sequences
Description: Create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences. Specifically, allows the user to programmatically generate helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of alpha-helical oligopeptides. See Wadhwa RR, et al. (2018) <doi:10.21105/joss.01008> for more information.
Author: Raoul Wadhwa [cre, aut], Regina Stevens-Truss [aut], Vigneshwar Subramanian [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>

Diff between helixvis versions 0.9.1 dated 2018-06-25 and 1.0.1 dated 2018-11-13

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Package double.truncation updated to version 1.2 with previous version 1.1 dated 2018-08-01

Title: Analysis of Doubly-Truncated Data
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models. Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>. Parametric models from the special exponential family (SEF) are based on Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
Author: Takeshi Emura, Ya-Hsuan Hu
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between double.truncation versions 1.1 dated 2018-08-01 and 1.2 dated 2018-11-13

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Package BiocManager updated to version 1.30.4 with previous version 1.30.3 dated 2018-10-10

Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>

Diff between BiocManager versions 1.30.3 dated 2018-10-10 and 1.30.4 dated 2018-11-13

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Package quadmesh updated to version 0.2.0 with previous version 0.1.0 dated 2016-06-13

Title: Quadrangle Mesh
Description: Create a standard quadrangle mesh from 'raster' data for flexible plotting and conversion to other mesh forms. The standard output 'quadmesh' is an 'mesh3d' object used by the 'rgl' package. This is used for plotting raster data in 3D with or without textures, and allows the application of a map projection without data loss.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

Diff between quadmesh versions 0.1.0 dated 2016-06-13 and 0.2.0 dated 2018-11-13

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Package textfeatures (with last version 0.2.0) was removed from CRAN

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

2018-10-29 0.2.0
2018-03-06 0.1.1

Permanent link
Package rdflib updated to version 0.2.0 with previous version 0.1.0 dated 2018-03-09

Title: Tools to Manipulate and Query Semantic Data
Description: The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Bryce Mecum [rev] (<https://orcid.org/0000-0002-0381-3766>), Anna Krystalli [rev] (<https://orcid.org/0000-0002-2378-4915>), Viktor Senderov [ctb] (<https://orcid.org/0000-0003-3340-5963>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between rdflib versions 0.1.0 dated 2018-03-09 and 0.2.0 dated 2018-11-13

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Package enveomics.R updated to version 1.4.2 with previous version 1.4.1 dated 2018-09-10

Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>

Diff between enveomics.R versions 1.4.1 dated 2018-09-10 and 1.4.2 dated 2018-11-13

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Mon, 12 Nov 2018

Package roptim updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-18

Title: General Purpose Optimization in R using C++
Description: Perform general purpose optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms ('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B' and 'SANN') underlying optim().
Author: Yi Pan [aut, cre]
Maintainer: Yi Pan <ypan1988@gmail.com>

Diff between roptim versions 0.1.1 dated 2018-10-18 and 0.1.2 dated 2018-11-12

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Package mlflow updated to version 0.8.0 with previous version 0.7.0 dated 2018-10-06

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

Diff between mlflow versions 0.7.0 dated 2018-10-06 and 0.8.0 dated 2018-11-12

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Package rpostgis updated to version 1.4.2 with previous version 1.4.1 dated 2018-08-17

Title: R Interface to a 'PostGIS' Database
Description: Provides an interface between R and 'PostGIS'-enabled 'PostgreSQL' databases to transparently transfer spatial data. Both vector (points, lines, polygons) and raster data are supported in read and write modes. Also provides convenience functions to execute common procedures in 'PostgreSQL/PostGIS'.
Author: Mathieu Basille [aut], David Bucklin [aut, cre]
Maintainer: David Bucklin <david.bucklin@gmail.com>

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Package PMCMRplus updated to version 1.4.1 with previous version 1.4.0 dated 2018-08-15

Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended
Description: For one-way layout experiments the one-way ANOVA can be performed as an omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test, Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally distributed residuals and equal within variance are available. Furthermore, all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for normally distributed residuals and heterogeneous variances are provided. Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one tests is provided for non-normally distributed residuals and homogeneous variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and all-pairs tests (Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test, Dunn test, U-test) are given for the analysis of variance by ranks. Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra test, Spearman test) are included. In addition, a Friedman-test for one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack test for unbalanced CRBD is provided with consequent all-pairs tests (Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and many-to-one tests (Nemenyi test, Demsar test, Exact test). A trend can be tested with Pages's test. Durbin's test for a two-way balanced incomplete block design (BIBD) is given in this package as well as Gore's test for CRBD with multiple observations per cell is given. Outlier tests, Mandel's k- and h statistic as well as functions for Type I error and Power analysis as well as generic summary, print and plot methods are provided.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

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Package FSelectorRcpp updated to version 0.3.0 with previous version 0.2.1 dated 2018-08-02

Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning. In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf> with a sparse matrix support. It is also equipped with a parallel backend.
Author: Zygmunt Zawadzki [aut, cre], Marcin Kosinski [aut], Krzysztof Slomczynski [ctb], Damian Skrzypiec [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

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Package rsconnect updated to version 0.8.11 with previous version 0.8.8 dated 2018-03-08

Title: Deployment Interface for R Markdown Documents and Shiny Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'RStudio Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.
Author: JJ Allaire
Maintainer: Jonathan McPherson <jonathan@rstudio.com>

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Package QGglmm updated to version 0.7.2 with previous version 0.7.1 dated 2018-06-15

Title: Estimate Quantitative Genetics Parameters from Generalised Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil <bonamy@horus.ens.fr>
Maintainer: Pierre de Villemereuil <bonamy@horus.ens.fr>

Diff between QGglmm versions 0.7.1 dated 2018-06-15 and 0.7.2 dated 2018-11-12

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Package emuR updated to version 1.1.1 with previous version 1.1.0 dated 2018-10-26

Title: Main Package of the EMU Speech Database Management System
Description: Provides the next iteration of the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre], Klaus Jaensch [aut, ctb], Steve Cassidy [aut, ctb], Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>

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Package trialr updated to version 0.0.5 with previous version 0.0.4 dated 2018-10-24

Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in 'RStan' and R. Some designs are implemented in R for the first time (e.g. 'EffTox' by Thall and Cook, 2004, <https://biostatistics.mdanderson.org/softwaredownload/SingleSoftware.aspx?Software_Id=2>). Given the emphasis on flexibility in Bayesian analysis, the implementations in a common language and style may serve as a cookbook to encourage the use of Bayesian methods in trials. Compiled 'RStan' models are provided in addition to helper classes and functions to perform simulations and inference on observed trial outcomes. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a published Bayesian design you want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre], Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>

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Package morse updated to version 3.2.0 with previous version 3.1.1 dated 2018-06-12

Title: Modelling Tools for Reproduction and Survival Data in Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of toxicity test data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment.
Author: Virgile Baudrot [aut], Sandrine Charles [aut], Marie Laure Delignette-Muller [aut], Wandrille Duchemin [ctb], Benoit Goussen [ctb], Guillaume Kon-Kam-King [ctb], Christelle Lopes [ctb], Philippe Ruiz [aut], Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>

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Package model4you updated to version 0.9-3 with previous version 0.9-2 dated 2018-06-15

Title: Stratified and Personalised Models Based on Model-Based Trees and Forests
Description: Model-based trees for subgroup analyses in clinical trials and model-based forests for the estimation and prediction of personalised treatment effects (personalised models). Currently partitioning of linear models, lm(), generalised linear models, glm(), and Weibull models, survreg(), is supported. Advanced plotting functionality is supported for the trees and a test for parameter heterogeneity is provided for the personalised models. For details on model-based trees for subgroup analyses see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for details on model-based forests for estimation of individual treatment effects see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre], Achim Zeileis [aut], Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>

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Package googleVis updated to version 0.6.3 with previous version 0.6.2 dated 2017-01-01

Title: R Interface to Google Charts
Description: R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

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Package fastLink updated to version 0.5.0 with previous version 0.4.0 dated 2018-05-15

Title: Fast Probabilistic Record Linkage with Missing Data
Description: Implements a Fellegi-Sunter probabilistic record linkage model that allows for missing data and the inclusion of auxiliary information. This includes functionalities to conduct a merge of two datasets under the Fellegi-Sunter model using the Expectation-Maximization algorithm. In addition, tools for preparing, adjusting, and summarizing data merges are included. The package implements methods described in Enamorado, Fifield, and Imai (2017) ''Using a Probabilistic Model to Assist Merging of Large-scale Administrative Records'', available at <http://imai.princeton.edu/research/linkage.html>.
Author: Ted Enamorado [aut, cre], Ben Fifield [aut], Kosuke Imai [aut]
Maintainer: Ted Enamorado <fastlinkr@gmail.com>

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Package RcppThread updated to version 0.5.2 with previous version 0.5.0 dated 2018-11-02

Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>

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Package ChainLadder updated to version 0.2.8 with previous version 0.2.7 dated 2018-10-16

Title: Statistical Methods and Models for Claims Reserving in General Insurance
Description: Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance, including those to estimate the claims development result as required under Solvency II.
Author: Markus Gesmann [aut, cre], Daniel Murphy [aut], Yanwei (Wayne) Zhang [aut], Alessandro Carrato [aut], Giuseppe Crupi [ctb], Christophe Dutang [ctb], Arnaud Lacoume [ctb], Arthur Charpentier [ctb], Mario Wuthrich [aut], Fabio Concina [aut], Eric Dal Moro [aut], Yuriy Krvavych [ctb], Vincent Goulet [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

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Package bhrcr updated to version 1.0.2 with previous version 1.0.1 dated 2018-08-28

Title: Bayesian Hierarchical Regression on Clearance Rates in the Presence of Lag and Tail Phases
Description: An implementation of the Bayesian Clearance Estimator (Fogarty et al. (2015) <doi:10.1111/biom.12307>). It takes serial measurements of a response on an individual (e.g., parasite load after treatment) that is decaying over time and performs Bayesian hierarchical regression of the clearance rates on the given covariates. This package provides tools to calculate WWARN PCE (WorldWide Antimalarial Resistance Network's Parasite Clearance Estimator) estimates of the clearance rates as well.
Author: Colin B. Fogarty [cre] <cfogarty@mit.edu>, Saeed Sharifi-Malvajerdi [aut] <saeedsh@wharton.upenn.edu>, Feiyu Zhu [aut] <feiyuzhu@sas.upenn.edu>
Maintainer: Colin B. Fogarty <cfogarty@mit.edu>

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Package PResiduals updated to version 0.2-6 with previous version 0.2-5 dated 2017-10-06

Title: Probability-Scale Residuals and Residual Correlations
Description: Computes probability-scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data.
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Bryan Shepherd <bryan.shepherd@VANDERBILT.EDU>

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Package live updated to version 1.5.9 with previous version 1.5.8 dated 2018-09-24

Title: Local Interpretable (Model-Agnostic) Visual Explanations
Description: Interpretability of complex machine learning models is a growing concern. This package helps to understand key factors that drive the decision made by complicated predictive model (so called black box model). This is achieved through local approximations that are either based on additive regression like model or CART like model that allows for higher interactions. The methodology is based on Tulio Ribeiro, Singh, Guestrin (2016) <doi:10.1145/2939672.2939778>. More details can be found in Staniak, Biecek (2018) <arXiv:1804.01955>.
Author: Mateusz Staniak [cre, aut], Przemysław Biecek [aut]
Maintainer: Mateusz Staniak <mateusz.staniak@math.uni.wroc.pl>

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Package DesignLibrary updated to version 0.1.2 with previous version 0.1.1 dated 2018-08-25

Title: Library of Research Designs
Description: A simple interface to build designs using the package 'DeclareDesign'. In one line of code, users can specify the parameters of individual designs and diagnose their properties. The designers can also be used to compare performance of a given design across a range of combinations of parameters, such as effect size, sample size, and assignment probabilities.
Author: Graeme Blair [aut], Jasper Cooper [aut, cre], Alexander Coppock [aut], Macartan Humphreys [aut], Clara Bicalho [aut], Neal Fultz [aut], Lily Medina [aut]
Maintainer: Jasper Cooper <jjc2247@columbia.edu>

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Package visualFields updated to version 0.5.5 with previous version 0.5.4 dated 2018-06-20

Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch <imarinfr@optocom.es>
Maintainer: Ivan Marin-Franch <imarinfr@optocom.es>

Diff between visualFields versions 0.5.4 dated 2018-06-20 and 0.5.5 dated 2018-11-12

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New package pvar with initial version 2.2.4
Package: pvar
Version: 2.2.4
Title: Calculation and Application of p-Variation
Date: 2018-11-12
Author: Vygantas Butkus
Maintainer: Vygantas Butkus <Vygantas.Butkus@gmail.com>
Description: The calculation of p-variation of the finite sample data. This package is a realisation of the procedure described in Butkus, V. & Norvaisa, R. Lith Math J (2018). <doi: 10.1007/s10986-018-9414-3> The formal definitions and reference into literature are given in vignette.
LazyData: yes
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp
Suggests: e1071, testthat, knitr, formatR,
VignetteBuilder: knitr
License: GPL-2
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2018-11-12 11:45:28 UTC; vygantas
Repository: CRAN
Date/Publication: 2018-11-12 13:00:09 UTC

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Package MetabolomicsBasics updated to version 1.1 with previous version 1.0 dated 2018-03-23

Title: Basic Functions to Investigate Metabolomics Data Matrices
Description: A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>

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Package xROI updated to version 0.9.11 with previous version 0.9.10 dated 2018-11-02

Title: Delineate Region of Interests (ROI's) and Extract Time-Series Data from Digital Repeat Photography Images
Description: Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
Author: Bijan Seyednasrollah, Thomas Milliman, Andrew D. Richardson
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>

Diff between xROI versions 0.9.10 dated 2018-11-02 and 0.9.11 dated 2018-11-12

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Package trekfont updated to version 0.9.3 with previous version 0.9.2 dated 2018-05-23

Title: Star Trek Fonts Collection
Description: Provides a collection of true type and open type Star Trek-themed fonts.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

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Package telegram.bot updated to version 2.1.0 with previous version 2.0.0 dated 2018-11-10

Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API' <http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>

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Package STARTS updated to version 0.5-28 with previous version 0.4-24 dated 2018-06-08

Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>, <DOI:10.1037/10409-008>. Penalized maximum likelihood estimation and Markov Chain Monte Carlo estimation are also provided, see Luedtke, Robitzsch and Wagner (2018) <DOI:10.1037/met0000155>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between STARTS versions 0.4-24 dated 2018-06-08 and 0.5-28 dated 2018-11-12

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Package shinyFiles updated to version 0.7.2 with previous version 0.7.1 dated 2018-09-18

Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut], Vincent Nijs [aut], Thomas Schaffner [aut], Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between shinyFiles versions 0.7.1 dated 2018-09-18 and 0.7.2 dated 2018-11-12

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Package RSAGA updated to version 1.3.0 with previous version 1.2.0 dated 2018-07-04

Title: SAGA Geoprocessing and Terrain Analysis
Description: Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from <http://sourceforge.net/projects/saga-gis/>.
Author: Alexander Brenning [aut, cre] (<https://orcid.org/0000-0001-6640-679X>), Donovan Bangs [aut], Marc Becker [aut], Patrick Schratz [ctb] (<https://orcid.org/0000-0003-0748-6624>), Fabian Polakowski [ctb]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>

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Package rmweather updated to version 0.1.3 with previous version 0.1.2 dated 2018-07-16

Title: Tools to Conduct Meteorological Normalisation on Air Quality Data
Description: An integrated set of tools to allow data users to conduct meteorological normalisation on air quality data. This meteorological normalisation technique uses predictive random forest models to remove variation of pollutant concentrations so trends and interventions can be explored in a robust way. For examples, see Grange et al. (2018) <doi:10.5194/acp-18-6223-2018> and Grange and Carslaw (2019) <doi:10.1016/j.scitotenv.2018.10.344>.
Author: Stuart K. Grange [cre, aut] (<https://orcid.org/0000-0003-4093-3596>)
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>

Diff between rmweather versions 0.1.2 dated 2018-07-16 and 0.1.3 dated 2018-11-12

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Package reqres updated to version 0.2.2 with previous version 0.2.1 dated 2017-10-25

Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating appropriate responses this package provides two classes to handle a lot of the housekeeping involved in working with http exchanges. The infrastructure builds upon the 'rook' specification and is thus well suited to be combined with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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New package parsnip with initial version 0.0.1
Package: parsnip
Version: 0.0.1
Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', etc).
Authors@R: c( person("Max", "Kuhn", , "max@rstudio.com", c("aut", "cre")), person("Davis", "Vaughan", , "davis@rstudio.com", c("aut")), person("RStudio", role = "cph"))
Maintainer: Max Kuhn <max@rstudio.com>
URL: https://tidymodels.github.io/parsnip
BugReports: https://github.com/tidymodels/parsnip/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
ByteCompile: true
VignetteBuilder: knitr
Depends: R (>= 2.10)
Imports: dplyr, rlang (>= 0.3.0.1), purrr, utils, tibble, generics, glue, magrittr, stats, tidyr, globals
RoxygenNote: 6.1.0.9000
Suggests: testthat, knitr, rmarkdown, survival, keras, xgboost, covr, sparklyr
NeedsCompilation: no
Packaged: 2018-11-05 03:07:44 UTC; max
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], RStudio [cph]
Repository: CRAN
Date/Publication: 2018-11-12 10:10:06 UTC

More information about parsnip at CRAN
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Package MLML2R updated to version 0.3.1 with previous version 0.3.0 dated 2018-09-30

Title: Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Description: Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2018, to appear).
Author: Samara Kiihl [aut, cre], Maria Jose Martinez-Garrido [aut], Arce Domingo-Relloso [aut], Jose Bermudez [aut], Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>

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New package MBTAr with initial version 2.0.0
Package: MBTAr
Type: Package
Title: Access Data from the Massachusetts Bay Transit Authority (MBTA) Web API
Version: 2.0.0
Authors@R: person("Justin", "de Benedictis-Kessner", email = "justindbk@gmail.com", role = c("aut", "cre"))
BugReports: https://github.com/justindbk/MBTAr/issues
Depends: R (>= 3.4.0)
LazyData: true
Description: Access to the MBTA's performance API for R. Creates an easy-to-use bundle of functions to work with all the built-in calls to the MBTA performance API, and some to work with the GTFS-compatible API V3 which replaced some functionality from the old performance API. Allows users to download realtime tracking data in dataframe format that is manipulable in standard R analytics functions. Pulls performance statistics in both realtime and for historical dates and trips (after July 2015).
License: GPL-3
Imports: jsonlite
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-11 20:10:47 UTC; justin
Author: Justin de Benedictis-Kessner [aut, cre]
Maintainer: Justin de Benedictis-Kessner <justindbk@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-12 10:00:23 UTC

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Package fingertipsR updated to version 0.2.0 with previous version 0.1.9 dated 2018-08-31

Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre], Julian Flowers [aut, ctb], Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>), Duncan Gormansway [ctb], Carl Ganz [ctb], David Whiting [ctb], Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>

Diff between fingertipsR versions 0.1.9 dated 2018-08-31 and 0.2.0 dated 2018-11-12

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Package ffmanova updated to version 0.9.1 with previous version 0.2-2 dated 2012-12-01

Title: Fifty-Fifty MANOVA
Description: General linear modeling with multiple responses (MANCOVA). An overall p-value for each model term is calculated by the 50-50 MANOVA method, which handles collinear responses. Rotation testing is used to compute adjusted single response p-values according to familywise error rates and false discovery rates.
Author: Øyvind Langsrud [aut, cre], Bjørn-Helge Mevik [aut]
Maintainer: Øyvind Langsrud <oyl@ssb.no>

Diff between ffmanova versions 0.2-2 dated 2012-12-01 and 0.9.1 dated 2018-11-12

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Package Directional updated to version 3.4 with previous version 3.3 dated 2018-07-11

Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

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Package RJSONIO updated to version 1.3-1 with previous version 1.3-0 dated 2014-07-28

Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang [aut, cre] (<https://orcid.org/0000-0003-0159-1546>), ninja9578 [aut] (Author of included libjson sources)
Maintainer: ORPHANED

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Package qrmtools updated to version 0.0-10 with previous version 0.0-9 dated 2018-04-28

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], Alexander J. McNeil [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

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Package febr updated to version 1.0.1 with previous version 1.0-0 dated 2018-03-09

Title: Free Brazilian Repository for Open Soil Data
Description: Making the access to the Free Brazilian Repository for Open Soil Data <http://www.ufsm.br/febr/> as easy as possible.
Author: Alessandro Samuel-Rosa [aut, cre] (<https://orcid.org/0000-0003-0877-1320>), Universidade Federal de Santa Maria [fnd], Universidade Tecnológica Federal do Paraná [fnd]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

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Sun, 11 Nov 2018

Package NCmisc updated to version 1.1.6 with previous version 1.1.5 dated 2017-01-03

Title: Miscellaneous Functions for Creating Adaptive Functions and Scripts
Description: A set of handy functions. Includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>

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Package Rcrawler updated to version 0.1.9-1 with previous version 0.1.8-0 dated 2018-10-03

Title: Web Crawler and Scraper
Description: Performs parallel web crawling and web scraping. It is designed to crawl, parse and store web pages to produce data that can be directly used for analysis application. For details see Khalil and Fakir (2017) <DOI:10.1016/j.softx.2017.04.004>.
Author: Salim Khalil [aut, cre] (<https://orcid.org/0000-0002-7804-4041>)
Maintainer: Salim Khalil <khalilsalim1@gmail.com>

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Package phenocamapi updated to version 0.1.2 with previous version 0.1.1 dated 2018-11-04

Title: Interacting with the PhenoCam Data and API
Description: A bundle to facilitate working with PhenoCam timeseries and data. The user would be able to obtain phenological time-series and site metadata from the PhenoCam network <https://phenocam.sr.unh.edu/webcam/>.
Author: Bijan Seyednasrollah
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>

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Package expss updated to version 0.8.8 with previous version 0.8.7 dated 2018-06-14

Title: Tables with Labels and Some Useful Functions from Spreadsheets and 'SPSS' Statistics
Description: Package provides tabulation functions with support for 'SPSS'-style labels, multiple / nested banners, weights, multiple-response variables and significance testing. There are facilities for nice output of tables in 'knitr', 'Shiny', R and 'Jupyter' notebooks, '*.xlsx' files. Proper methods for labelled variables add value labels support to base R functions and to some functions from other packages. Additionally, the package offers useful functions for data processing in marketing research / social surveys - popular data transformation functions from 'SPSS' Statistics ('RECODE', 'COUNT', 'COMPUTE', 'DO IF', etc.) and 'Excel' ('COUNTIF', 'VLOOKUP', etc.). Package is intended to help people to move data processing from 'Excel'/'SPSS' to R.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>

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Package nandb updated to version 2.0.0 with previous version 1.0.1 dated 2018-05-08

Title: Number and Brightness Image Analysis
Description: Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package IRdisplay updated to version 0.6.1 with previous version 0.6 dated 2018-09-24

Title: 'Jupyter' Display Machinery
Description: An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>. Designed to be used from a running 'IRkernel' session <https://irkernel.github.io>.
Author: Thomas Kluyver [aut, cph], Philipp Angerer [aut, cph, cre], Jan Schulz [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>

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Package tables updated to version 0.8.7 with previous version 0.8.4 dated 2018-05-21

Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics. Output may be in LaTeX, HTML, plain text, or an R matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

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Package SpATS updated to version 1.0-9 with previous version 1.0-8 dated 2018-05-30

Title: Spatial Analysis of Field Trials with Splines
Description: Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.
Author: Maria Xose Rodriguez-Alvarez [aut, cre], Martin Boer [aut], Paul Eilers [aut], Fred van Eeuwijk [ctb]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>

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Package reportReg updated to version 0.3.0 with previous version 0.2.0 dated 2018-04-22

Title: An Easy Way to Report Regression Analysis
Description: Provides an easy way to report the results of regression analysis, including: 1. Proportional hazards regression from function 'coxph' of package 'survival'; 2. Conditional logistic regression from function 'clogit' of package 'survival'; 3. Ordered logistic regression from function 'polr' of package 'MASS'; 4. Binary logistic regression from function 'glm' of package 'stats'; 5. Linear regression from function 'lm' of package 'stats'; 6. Risk regression model for survival analysis with competing risks from function 'FGR' of package 'riskRegression'; 7. Multilevel model from function 'lme' of package 'nlme'.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

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Package ggpubr updated to version 0.1.9 with previous version 0.1.8 dated 2018-08-30

Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package hmm.discnp updated to version 2.1-3 with previous version 0.2-4 dated 2016-04-08

Title: Hidden Markov Models with Discrete Non-Parametric Observation Distributions
Description: Fits hidden Markov models with discrete non-parametric observation distributions to data sets. The observations may be univariate or bivariate. Simulates data from such models. Finds most probable underlying hidden states, the most probable sequences of such states, and the log likelihood of a collection of observations given the parameters of the model. Auxiliary predictors are accommodated in the univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package cAIC4 updated to version 0.6 with previous version 0.5 dated 2018-09-18

Title: Conditional Akaike Information Criterion for 'lme4'
Description: Provides functions for the estimation of the conditional Akaike information in generalized mixed-effect models fitted with (g)lmer() from 'lme4'.
Author: Benjamin Saefken and David Ruegamer, with contributions from Sonja Greven and Thomas Kneib
Maintainer: David Ruegamer <david.ruegamer@gmail.com>

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Package AMCTestmakeR updated to version 1.0.0 with previous version 0.1.0 dated 2017-03-29

Title: Generate LaTeX Code for Auto-Multiple-Choice (AMC)
Description: Generate code for use with the Optical Mark Recognition free software Auto Multiple Choice (AMC). More specifically, this package provides functions that use as input the question and answer texts, and output the LaTeX code for AMC.
Author: Nils Myszkowski
Maintainer: Nils Myszkowski <nmyszkowski@pace.edu>

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Package textcat updated to version 1.0-6 with previous version 1.0-5 dated 2017-02-20

Title: N-Gram Based Text Categorization
Description: Text categorization based on n-grams.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Johannes Rauch [aut], Christian Buchta [aut], Ingo Feinerer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package BGLR updated to version 1.0.8 with previous version 1.0.7 dated 2018-08-24

Title: Bayesian Generalized Linear Regression
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez,
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>

Diff between BGLR versions 1.0.7 dated 2018-08-24 and 1.0.8 dated 2018-11-11

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 DESCRIPTION              |   16 +-
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More information about BGLR at CRAN
Permanent link

Sat, 10 Nov 2018

Package RcppArmadillo updated to version 0.9.200.4.0 with previous version 0.9.100.5.0 dated 2018-08-16

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'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.9.100.5.0 dated 2018-08-16 and 0.9.200.4.0 dated 2018-11-10

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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp                 |    4 
 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_bones.hpp             |    2 
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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp               |  371 +++---
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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_cond.hpp                  |   25 
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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp                  |   13 
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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp                 |  129 ++
 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_trig.hpp                  |   46 
 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_bones.hpp         |    3 
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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp          |    2 
 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_bones.hpp             |   20 
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 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_bones.hpp       |   13 
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Package rcmdcheck updated to version 1.3.2 with previous version 1.3.1 dated 2018-11-05

Title: Run 'R CMD check' from 'R' and Capture Results
Description: Run 'R CMD check' from 'R' programmatically, and capture the results of the individual checks.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between rcmdcheck versions 1.3.1 dated 2018-11-05 and 1.3.2 dated 2018-11-10

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Package jmcm updated to version 0.2.1 with previous version 0.2.0 dated 2018-11-04

Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Armadillo' C++ library for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre], Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>

Diff between jmcm versions 0.2.0 dated 2018-11-04 and 0.2.1 dated 2018-11-10

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Package Ruchardet updated to version 0.0-3.1 with previous version 0.0-3 dated 2014-02-07

Title: R Package to Detect Character Encoding
Description: R port of 'universalchardet', that is the encoding detector library of Mozilla.
Author: Heewon Jeon
Maintainer: ORPHANED

Diff between Ruchardet versions 0.0-3 dated 2014-02-07 and 0.0-3.1 dated 2018-11-10

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Package tcpl updated to version 2.0.0 with previous version 1.4.3 dated 2018-05-20

Title: ToxCast Data Analysis Pipeline
Description: A set of tools for processing and modeling high-throughput and high-content chemical screening data. The package was developed for the the chemical screening data generated by the US EPA ToxCast program, but can be used for diverse chemical screening efforts.
Author: Richard S Judson [cre, ths], Dayne L Filer [aut], Jason Brown [ctb], Parth Kothiya [ctb], Woodrow R Setzer [ctb], Matthew T Martin [ctb, ths]
Maintainer: Richard S Judson <Judson.Richard@epa.gov>

Diff between tcpl versions 1.4.3 dated 2018-05-20 and 2.0.0 dated 2018-11-10

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Package Rtsne updated to version 0.15 with previous version 0.13 dated 2017-04-14

Title: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
Description: An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten (see <https://github.com/lvdmaaten/bhtsne/> for more information on the original implementation).
Author: Jesse Krijthe [aut, cre], Laurens van der Maaten [cph] (Author of original C++ code)
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>

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Package rstanarm updated to version 2.18.2 with previous version 2.18.1 dated 2018-10-21

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Imad Ali [ctb], Sam Brilleman [ctb], Jacqueline Buros Novik [ctb] (R/stan_jm.R), AstraZeneca [ctb] (R/stan_jm.R), Trustees of Columbia University [cph], Simon Wood [cph] (R/stan_gamm4.R), R Core Deveopment Team [cph] (R/stan_aov.R), Douglas Bates [cph] (R/pp_data.R), Martin Maechler [cph] (R/pp_data.R), Ben Bolker [cph] (R/pp_data.R), Steve Walker [cph] (R/pp_data.R), Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R), William Venables [cph] (R/stan_polr.R), Paul-Christian Burkner [cph] (R/misc.R), Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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Package lme4 updated to version 1.1-19 with previous version 1.1-18-1 dated 2018-08-17

Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>), Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>), Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>), Rune Haubo Bojesen Christensen [ctb] (<https://orcid.org/0000-0002-4494-3399>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Bin Dai [ctb], Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>), Gabor Grothendieck [ctb], Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>), John Fox [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>

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Package MetaStan (with last version 0.0.1) was removed from CRAN

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

2018-09-30 0.0.1

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Package bigFastlm (with last version 0.0.2) was removed from CRAN

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

2017-03-12 0.0.2
2016-10-06 0.0.1

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Package bayesLopod (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:

2018-01-04 1.0.1
2017-11-27 1.0.0

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Package walkr (with last version 0.3.4) was removed from CRAN

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

2017-02-24 0.3.4

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Package interep updated to version 0.2.0 with previous version 0.1.0 dated 2018-09-03

Title: Interaction Analysis of Repeatedly Measured Data
Description: Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Fei Zhou, Jie Ren, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Fei Zhou <feiz@ksu.edu>

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Package REndo updated to version 2.0.0 with previous version 1.3 dated 2017-11-08

Title: Fitting Linear Models with Endogenous Regressors using Latent Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches. The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroskedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized method of moment approach that deals with endogeneity in a multilevel setting. These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed. Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut], Markus Meierer [aut], Rene Algesheimer [aut], Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>

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Package gastempt updated to version 0.4.3 with previous version 0.4.01 dated 2017-05-10

Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or scintigraphic measurements using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>

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Package furniture updated to version 1.8.7 with previous version 1.8.0 dated 2018-09-19

Title: Furniture for Quantitative Scientists
Description: Contains three main functions (i.e., three pieces of furniture): table1() which produces a well-formatted table of descriptives common as Table 1 in research articles, tableC() which produces a well-formatted table of correlations, tableF() which provides frequency counts, and washer() which is helpful in cleaning up the data. These furniture-themed functions are designed to simplify common tasks in quantitative analysis. Other data summary and cleaning tools are also available.
Author: Tyson S. Barrett [aut, cre] (<https://orcid.org/0000-0002-2137-1391>), Emily Brignone [aut], Daniel J. Laxman [aut]
Maintainer: Tyson S. Barrett <t.barrett@aggiemail.usu.edu>

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Package sparkavro updated to version 0.2.0 with previous version 0.1.0 dated 2017-11-17

Title: Load Avro file into 'Apache Spark'
Description: Load Avro Files into 'Apache Spark' using 'sparklyr'. This allows to read files from 'Apache Avro' <https://avro.apache.org/>.
Author: Aki Ariga
Maintainer: Aki Ariga <chezou@gmail.com>

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Package telegram.bot updated to version 2.0.0 with previous version 1.0.0 dated 2018-02-12

Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API' <http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>

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Package VICmodel updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-06

Title: The Variable Infiltration Capacity (VIC) Model
Description: The Variable Infiltration Capacity (VIC) model is a macroscale hydrologic model that solves full water and energy balances, originally developed by Xu Liang at the University of Washington (UW). The version of VIC source code used is of 5.0.1 on <https://github.com/UW-Hydro/VIC/>, see Hamman et al. (2018). Development and maintenance of the current official version of the VIC model at present is led by the UW Hydro (Computational Hydrology group) in the Department of Civil and Environmental Engineering at UW. VIC is a research model and in its various forms it has been applied to most of the major river basins around the world, as well as globally. If you make use of this model, please acknowledge the appropriate references listed in the help page of this package or on the references page <http://vic.readthedocs.io/en/master/Documentation/References/> of the VIC official documentation website. These should include Liang et al. (1994) plus any references relevant to the features you are using Reference: Liang, X., D. P. Lettenmaier, E. F. Wood, and S. J. Burges (1994), A simple hydrologically based model of land surface water and energy fluxes for general circulation models, J. Geophys. Res., 99(D7), 14415-14428, <doi:10.1029/94JD00483>. Hamman et al. (2018) about VIC 5.0.1 also can be considered: Hamman, J. J., Nijssen, B., Bohn, T. J., Gergel, D. R., and Mao, Y. (2018), The Variable Infiltration Capacity model version 5 (VIC-5): infrastructure improvements for new applications and reproducibility, Geosci. Model Dev., 11, 3481-3496, <doi:10.5194/gmd-11-3481-2018>.
Author: Ruida Zhong [aut, cre], Xiaohong Chen [aut, ctb], Zhaoli Wang [aut, ctb], Chengguang Lai [aut, ctb], Joseph J Hamman [ctb] (Contributor and maintainer of VIC source code), Keith Cherkauer [ctb]
Maintainer: Ruida Zhong <zrd2017@163.com>

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Package spTimer updated to version 3.3 with previous version 3.2 dated 2018-10-25

Title: Spatio-Temporal Bayesian Modelling
Description: Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems. Bakar and Sahu (2015) <doi:10.18637/jss.v063.i15>.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Shuvo Bakar <shuvo.bakar@gmail.com>

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Package Rmpi updated to version 0.6-8 with previous version 0.6-7 dated 2018-04-11

Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>

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Package dplyr updated to version 0.7.8 with previous version 0.7.7 dated 2018-10-16

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package SpatialVS updated to version 1.1 with previous version 1.0 dated 2018-09-30

Title: Spatial Variable Selection
Description: Perform variable selection for the spatial Poisson regression model under the adaptive elastic net penalty. Spatial count data with covariates is the input. We use a spatial Poisson regression model to link the spatial counts and covariates. For maximization of the likelihood under adaptive elastic net penalty, we implemented the penalized quasi-likelihood (PQL) and the approximate penalized loglikelihood (APL) methods. The proposed methods can automatically select important covariates, while adjusting for possible spatial correlations among the responses. More details are available in Xie et al. (2018, <arXiv:1809.06418>). The package also contains the Lyme disease dataset, which consists of the disease case data from 2006 to 2011, and demographic data and land cover data in Virginia. The Lyme disease case data were collected by the Virginia Department of Health. The demographic data (e.g., population density, median income, and average age) are from the 2010 census. Land cover data were obtained from the Multi-Resolution Land Cover Consortium for 2006.
Author: Yili Hong, Li Xu, Yimeng Xie, and Zhongnan Jin
Maintainer: Yili Hong <yilihong@vt.edu>

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Package lslx updated to version 0.6.4 with previous version 0.6.3 dated 2018-08-09

Title: Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood
Description: Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) with LASSO or minimax concave penalty (MCP).
Author: Po-Hsien Huang [cre, aut], Wen-Hsin Hu [aut]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>

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Package aphid updated to version 1.3.1 with previous version 1.3.0 dated 2018-10-09

Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>

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Fri, 09 Nov 2018

Package rmytarget updated to version 1.1.1 with previous version 1.1 dated 2018-09-28

Title: Load Data from 'MyTarget API'
Description: Allows work with 'MyTarget API' <https://target.my.com/adv/api-marketing/> and load data by ads, campaigns and statistic from your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package rockchalk updated to version 1.8.129 with previous version 1.8.117 dated 2018-09-12

Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation of regression analysis. These functions are used to produce the statistics lectures in <http://pj.freefaculty.org/guides>. Includes regression diagnostics, regression tables, and plots of interactions and "moderator" variables. The emphasis is on "mean-centered" and "residual-centered" predictors. The vignette 'rockchalk' offers a fairly comprehensive overview. The vignette 'Rstyle' has advice about coding in R. The package title 'rockchalk' refers to our school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre], Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>

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Package ZeBook updated to version 1.1 with previous version 1.0 dated 2018-03-13

Title: Working with Dynamic Models for Agriculture and Environment
Description: R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (U.of Florida), Francois Brun (ACTA). 3rd edition 2018-09-27.
Author: Francois Brun (ACTA), David Makowski (INRA), Daniel Wallach (INRA), James W. Jones (U.of Florida).
Maintainer: Francois Brun <francois.brun@acta.asso.fr>

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Package rfishbase updated to version 3.0.0 with previous version 2.1.2 dated 2017-04-19

Title: R Interface to 'FishBase'
Description: A programmatic interface to <http://www.fishbase.org>, re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to <http://www.sealifebase.org> data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Duncan Temple Lang [aut], Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package ctsem updated to version 2.7.4 with previous version 2.6.5 dated 2018-06-25

Title: Continuous Time Structural Equation Modelling
Description: A hierarchical, multivariate, continuous (and discrete) time dynamic modelling package for panel and time series data, using stochastic differential equations. Contains a faster frequentist set of functions using OpenMx for single subject and mixed-effects (random intercepts only) structural equation models, or a hierarchical Bayesian implementation using Stan that allows for random effects and non-linearity over all model parameters. Allows for modelling of multiple noisy measurements of multiple stochastic processes, time varying input / event covariates, and time invariant covariates used to predict the parameters.
Author: Charles Driver [aut, cre, cph], Manuel Voelkle [aut, cph], Han Oud [aut, cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>

Diff between ctsem versions 2.6.5 dated 2018-06-25 and 2.7.4 dated 2018-11-09

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More information about ctsem at CRAN
Permanent link

Package arsenal updated to version 1.5.0 with previous version 1.4.0 dated 2018-09-18

Title: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of a categorical variable; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on the same endpoint for many variables (univariate or adjusted for standard covariates); freqlist(), a powerful frequency table across many categorical variables; compare.data.frame(), the S3 method for comparing data.frames; and write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre], Jason Sinnwell [aut], Elizabeth Atkinson [aut], Tina Gunderson [aut], Gregory Dougherty [aut], Patrick Votruba [ctb], Ryan Lennon [ctb], Andrew Hanson [ctb], Krista Goergen [ctb], Emily Lundt [ctb], Brendan Broderick [ctb]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>

Diff between arsenal versions 1.4.0 dated 2018-09-18 and 1.5.0 dated 2018-11-09

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More information about arsenal at CRAN
Permanent link

Package TMB updated to version 1.7.15 with previous version 1.7.14 dated 2018-06-23

Title: Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
Description: With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines 'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph], Brad Bell [cph], Hans Skaug [ctb], Arni Magnusson [ctb], Casper Berg [ctb], Anders Nielsen [ctb], Martin Maechler [ctb], Theo Michelot [ctb], Mollie Brooks [ctb], Alex Forrence [ctb], Christoffer Moesgaard Albertsen [ctb], Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>

Diff between TMB versions 1.7.14 dated 2018-06-23 and 1.7.15 dated 2018-11-09

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More information about TMB at CRAN
Permanent link

Package quickPlot updated to version 0.1.6 with previous version 0.1.5 dated 2018-10-01

Title: A System of Plotting Optimized for Speed and Modularity
Description: A high-level plotting system, built using 'grid' graphics, that is optimized for speed and modularity. This has great utility for quick visualizations when testing code, with the key benefit that visualizations are updated independently of one another.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>), Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>), Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

Diff between quickPlot versions 0.1.5 dated 2018-10-01 and 0.1.6 dated 2018-11-09

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Permanent link

Package IsoplotR updated to version 2.2 with previous version 2.1 dated 2018-10-20

Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 2.1 dated 2018-10-20 and 2.2 dated 2018-11-09

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Package dimRed updated to version 0.2.1 with previous version 0.2.0 dated 2018-11-08

Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction techniques from R packages and a common interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>

Diff between dimRed versions 0.2.0 dated 2018-11-08 and 0.2.1 dated 2018-11-09

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Package detrendr updated to version 0.6.0 with previous version 0.5.1 dated 2018-04-24

Title: Detrend Images
Description: Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This package contains functionality published in a 2016 paper <doi:10.1093/bioinformatics/btx434> but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package DeclareDesign updated to version 0.12.0 with previous version 0.10.0 dated 2018-07-29

Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of research designs before implementation using `DeclareDesign`. Ex ante declaration and diagnosis of designs can help researchers clarify the strengths and limitations of their designs and to improve their properties, and can help readers evaluate a research strategy prior to implementation and without access to results. It can also make it easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre], Jasper Cooper [aut], Alexander Coppock [aut], Macartan Humphreys [aut], Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

Diff between DeclareDesign versions 0.10.0 dated 2018-07-29 and 0.12.0 dated 2018-11-09

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Package antiword updated to version 1.3 with previous version 1.2 dated 2018-10-07

Title: Extract Text from Microsoft Word Documents
Description: Wraps the 'AntiWord' utility to extract text from Microsoft Word documents. The utility only supports the old 'doc' format, not the new xml based 'docx' format. Use the 'xml2' package to read the latter.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Adri van Os [cph] (Author 'antiword' utility)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between antiword versions 1.2 dated 2018-10-07 and 1.3 dated 2018-11-09

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More information about antiword at CRAN
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Package simmer updated to version 4.1.0 with previous version 4.0.1 dated 2018-09-10

Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation (DES) package for R. It is designed as a generic yet powerful framework. The architecture encloses a robust and fast simulation core written in 'C++' with automatic monitoring capabilities. It provides a rich and flexible R API that revolves around the concept of trajectory, a common path in the simulation model for entities of the same type. Documentation about 'simmer' is provided by several vignettes included in this package, via the paper by Ucar, Smeets & Azcorra (2018, <arXiv:1705.09746>), and the paper by Ucar, Hernández, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>); see 'citation("simmer")' for details.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>), Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>

Diff between simmer versions 4.0.1 dated 2018-09-10 and 4.1.0 dated 2018-11-09

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More information about simmer at CRAN
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New package ibs with initial version 1.4
Package: ibs
Type: Package
Title: Integral of B-Spline Functions
Version: 1.4
Date: 2018-11-06
Author: Feng Chen
Maintainer: Feng Chen <feng.chen@unsw.edu.au>
Description: Calculate B-spline basis functions with a given set of knots and order, or a B-spline function with a given set of knots and order and set of de Boor points (coefficients), or the integral of a B-spline function.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-11-06 23:16:47 UTC; Feng Chen
Repository: CRAN
Date/Publication: 2018-11-09 15:10:03 UTC

More information about ibs at CRAN
Permanent link

Package finalfit updated to version 0.8.8 with previous version 0.8.7 dated 2018-09-21

Title: Quickly Create Elegant Regression Results Tables and Plots when Modelling
Description: Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre], Tom Drake [aut], Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>

Diff between finalfit versions 0.8.7 dated 2018-09-21 and 0.8.8 dated 2018-11-09

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 finalfit-0.8.8/finalfit/NAMESPACE                                                                          |   19 
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Package dtangle updated to version 0.3.1 with previous version 0.3.0 dated 2018-07-05

Title: Cell Type Deconvolution from Gene Expressions
Description: Deconvolving cell types from high-throughput gene profiling data.
Author: Gregory Hunt
Maintainer: Gregory Hunt <gjhunt@umich.edu>

Diff between dtangle versions 0.3.0 dated 2018-07-05 and 0.3.1 dated 2018-11-09

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Package dfpk updated to version 3.5.1 with previous version 3.5.0 dated 2018-07-29

Title: Bayesian Dose-Finding Designs using Pharmacokinetics (PK) for Phase I Clinical Trials
Description: Statistical methods involving PK measures are provided, in the dose allocation process during a Phase I clinical trials. These methods, proposed by Ursino et al, (2017) <doi:10.1002/bimj.201600084>, enter pharmacokinetics (PK) in the dose finding designs in different ways, including covariates models, dependent variable or hierarchical models. This package provides functions to generate data from several scenarios and functions to run simulations which their objective is to determine the maximum tolerated dose (MTD).
Author: Artemis Toumazi [cre, aut], Sarah Zohar [aut], Moreno Ursino [aut], Trustees of Columbia University [cph] (R/stanmodels.R), French National Institute of Health and Medical Research [cph]
Maintainer: Artemis Toumazi <artemis.toumazi@gmail.com>

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Package bmlm updated to version 1.3.9 with previous version 1.3.8 dated 2018-10-17

Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre] (<https://orcid.org/0000-0001-5052-066X>)
Maintainer: Matti Vuorre <mv2521@columbia.edu>

Diff between bmlm versions 1.3.8 dated 2018-10-17 and 1.3.9 dated 2018-11-09

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Package bayesdfa updated to version 0.1.1 with previous version 0.1.0 dated 2018-09-19

Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic factor analysis is a dimension reduction tool for multivariate time series. 'bayesdfa' extends conventional dynamic factor models in several ways. First, extreme events may be estimated in the latent trend by modeling process error with a student-t distribution. Second, autoregressive and moving average components can be optionally included. Third, the estimated dynamic factors can be analyzed with hidden Markov models to evaluate support for latent regimes.
Author: Eric J. Ward [aut, cre], Sean C. Anderson [aut], Luis A. Damiano [aut], Mary E. Hunsicker, [ctb], Mike A. Litzow [ctb], Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>

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Package walker updated to version 0.2.3-1 with previous version 0.2.3 dated 2018-10-23

Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression coefficients can vary over time as random walks. Gaussian, Poisson, and binomial observations are supported. The Markov chain Monte Carlo computations are done using Hamiltonian Monte Carlo provided by Stan, using a state space representation of the model in order to marginalise over the coefficients for efficient sampling. For non-Gaussian models, walker uses the importance sampling type estimators based on approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package survHE updated to version 1.0.65 with previous version 1.0.64 dated 2018-10-19

Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners).
Author: Gianluca Baio [aut, cre]
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>

Diff between survHE versions 1.0.64 dated 2018-10-19 and 1.0.65 dated 2018-11-09

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Package seqmon updated to version 2.2 with previous version 2.1 dated 2016-10-12

Title: Group Sequential Design Class for Clinical Trials
Description: S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
Author: David A Schoenfeld, PhD and Hui Zheng, PhD
Maintainer: Hui Zheng <hzheng1@mgh.harvard.edu>

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Package Rfast updated to version 1.9.2 with previous version 1.9.1 dated 2018-07-20

Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. Reference: Tsagris M, Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>

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Package plinkQC updated to version 0.2.0 with previous version 0.1.1 dated 2018-11-06

Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals genotype at thousands of markers. 'plinkQC' facilitates genotype quality control for genetic association studies as described by Anderson and colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions accessible from 'R' and generates a per-individual and per-marker quality control report. Individuals and markers that fail the quality control can subsequently be removed to generate a new, clean dataset. Removal of individuals based on relationship status is optimised to retain as many individuals as possible in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah@ebi.ac.uk>

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Package Phase123 updated to version 2.0 with previous version 1.9 dated 2018-11-06

Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>

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Package modesto updated to version 0.1.1 with previous version 0.1.0 dated 2018-11-03

Title: Modeling and Analysis of Stochastic Systems
Description: Compute important quantities when we consider stochastic systems that are observed continuously. Such as, Cost model, Limiting distribution, Transition matrix, Transition distribution and Occupancy matrix. The methods are described, for example, Ross S. (2014), Introduction to Probability Models. Eleven Edition. Academic Press.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>

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Package MALDIrppa updated to version 1.0.1-2 with previous version 1.0.1 dated 2017-09-19

Title: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
Description: Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data.
Author: Javier Palarea-Albaladejo
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>

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Package jomo updated to version 2.6-5 with previous version 2.6-4 dated 2018-08-30

Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>

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Package idem updated to version 4.0 with previous version 3.5 dated 2018-04-12

Title: Inference in Randomized Controlled Trials with Death and Missingness
Description: In randomized studies involving severely ill patients, functional outcomes are often unobserved due to missed clinic visits, premature withdrawal or death. It is well known that if these unobserved functional outcomes are not handled properly, biased treatment comparisons can be produced. In this package, we implement a procedure for comparing treatments that is based on the composite endpoint of both the functional outcome and survival. The procedure was proposed in Wang et al. (2016) <DOI:10.1111/biom.12594>. It considers missing data imputation with a sensitivity analysis strategy to handle the unobserved functional outcomes not due to death.
Author: Chenguang Wang [aut, cre], Andrew Leroux [aut, cre], Elizabeth Colantuoni [aut], Daniel O Scharfstein [aut], Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>

Diff between idem versions 3.5 dated 2018-04-12 and 4.0 dated 2018-11-09

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Package idefix updated to version 0.3.3 with previous version 0.3.1 dated 2018-10-15

Title: Efficient Designs for Discrete Choice Experiments
Description: Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Crabbe M, Akinc D and Vandebroek M (2014) <doi:10.1016/j.trb.2013.11.008>.
Author: Frits Traets [aut, cre]
Maintainer: Frits Traets <frits.traets@kuleuven.be>

Diff between idefix versions 0.3.1 dated 2018-10-15 and 0.3.3 dated 2018-11-09

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Package glmmfields updated to version 0.1.1 with previous version 0.1.0 dated 2018-06-24

Title: Generalized Linear Mixed Models with Robust Random Fields for Spatiotemporal Modeling
Description: Implements Bayesian spatial and spatiotemporal models that optionally allow for extreme spatial deviations through time. 'glmmfields' uses a predictive process approach with random fields implemented through a multivariate-t distribution instead of the usual multivariate normal. Sampling is conducted with 'Stan'. References: Anderson and Ward (2018) <doi:10.1002/ecy.2403>.
Author: Sean C. Anderson [aut, cre], Eric J. Ward [aut], Trustees of Columbia University [cph]
Maintainer: Sean C. Anderson <sean@seananderson.ca>

Diff between glmmfields versions 0.1.0 dated 2018-06-24 and 0.1.1 dated 2018-11-09

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Package eggCounts updated to version 2.1-2 with previous version 2.1-1 dated 2018-10-16

Title: Hierarchical Modelling of Faecal Egg Counts
Description: An implementation of Bayesian hierarchical models for faecal egg count data to assess anthelmintic efficacy. Bayesian inference is done via MCMC sampling using Stan.
Author: Craig Wang [aut, cre] (<https://orcid.org/0000-0003-1804-2463>), Michaela Paul [aut], Tea Isler [ctb], Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>), Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R, R/stanmodels.R)
Maintainer: Craig Wang <craig.wang@uzh.ch>

Diff between eggCounts versions 2.1-1 dated 2018-10-16 and 2.1-2 dated 2018-11-09

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Package ddsPLS updated to version 1.0.3 with previous version 1.0.2 dated 2018-11-06

Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>

Diff between ddsPLS versions 1.0.2 dated 2018-11-06 and 1.0.3 dated 2018-11-09

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Package linguisticsdown updated to version 1.1.0 with previous version 1.0.1 dated 2018-09-30

Title: Easy Linguistics Document Writing with R Markdown
Description: Provides 'Shiny gadgets' to search, type, and insert IPA symbols into documents or scripts, requiring only knowledge about phonetics or 'X-SAMPA'. Also provides functions to facilitate the rendering of IPA symbols in 'LaTeX' and PDF format, making IPA symbols properly rendered in all output formats. A minimal R Markdown template for authoring Linguistics related documents is also bundled with the package.
Author: Yongfu Liao [aut, cre, cph] (<https://orcid.org/0000-0002-1814-2993>)
Maintainer: Yongfu Liao <liao961120@gmail.com>

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Package STMotif updated to version 1.0.1 with previous version 1.0.0 dated 2018-10-22

Title: Discovery of Motifs in Spatial-Time Series
Description: Allows to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
Author: Amin Bazaz [aut] (Polytech'Montpellier), Heraldo Borges [aut, cre] (CEFET/RJ), Eduardo Ogasawara [aut] (CEFET/RJ)
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>

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Package Gmisc updated to version 1.7 with previous version 1.6.4 dated 2018-09-19

Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories, flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>

Diff between Gmisc versions 1.6.4 dated 2018-09-19 and 1.7 dated 2018-11-09

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Package tmbstan updated to version 1.0.1 with previous version 1.0.0 dated 2017-12-19

Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects.
Author: Kasper Kristensen
Maintainer: Kasper Kristensen <kaskr@dtu.dk>

Diff between tmbstan versions 1.0.0 dated 2017-12-19 and 1.0.1 dated 2018-11-09

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Package Grid2Polygons (with last version 0.2.1) was removed from CRAN

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

2017-08-03 0.2.1
2017-02-08 0.1.6
2015-02-20 0.1-5
2013-08-31 0.1-4
2013-01-28 0.1-2
2012-05-27 0.1-0

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