Fri, 24 Aug 2018

Package gsynth updated to version 1.0.9 with previous version 1.0.6 dated 2017-10-16

Title: Generalized Synthetic Control Method
Description: Provides causal inference with interactive fixed-effect models. It imputes counterfactuals for each treated unit using control group information based on a linear interactive fixed effects model that incorporates unit-specific intercepts interacted with time-varying coefficients. This method generalizes the synthetic control method to the case of multiple treated units and variable treatment periods, and improves efficiency and interpretability. This version supports unbalanced panels and implements the matrix completion method. Main reference: Yiqing Xu (2017) <doi:10.1017/pan.2016.2>.
Author: Yiqing Xu, Licheng Liu
Maintainer: Yiqing Xu <yiqingxu@ucsd.edu>

Diff between gsynth versions 1.0.6 dated 2017-10-16 and 1.0.9 dated 2018-08-24

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New package calpassapi with initial version 0.0.1
Package: calpassapi
Title: R Interface to Access CalPASS API
Version: 0.0.1
Authors@R: person("Vinh", "Nguyen", email = "nguyenvq714@gmail.com", role = c("aut", "cre"))
Description: Implements methods for querying data from CalPASS using its API. CalPASS Plus. MMAP API V1. <https://mmap.calpassplus.org/docs/index.html>.
Depends: R (>= 3.4.0)
Imports: httr, dplyr, digest, jsonlite, stringr
License: GPL-3
URL: https://github.com/vinhdizzo/calpassapi
BugReports: https://github.com/vinhdizzo/calpassapi/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-24 22:21:04 UTC; vnguyen216
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-24 22:44:24 UTC

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New package twoway with initial version 0.6.2
Package: twoway
Type: Package
Title: Analysis of Two-Way Tables
Version: 0.6.2
Authors@R: c(person(given = "Michael", family = "Friendly", role=c("aut", "cre"), email="friendly@yorku.ca"), person(given = c("Richard", "M."), family = "Heiberger", role="aut", email="rmh@temple.edu"), person(given = "John", family = "Fox", role="ctb", email="jfox@mcmaster.ca") )
Author: Michael Friendly [aut, cre], Richard M. Heiberger [aut], John Fox [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Description: Carries out analyses of two-way tables with one observation per cell, together with graphical displays for an additive fit and a diagnostic plot for removable 'non-additivity' via a power transformation of the response. It implements Tukey's Exploratory Data Analysis methods, including a 1-degree-of-freedom test for row*column 'non-additivity', linear in the row and column effects.
URL: https://github.com/friendly/twoway
BugReports: https://github.com/friendly/twoway/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-20 19:29:49 UTC; Friendly
Repository: CRAN
Date/Publication: 2018-08-24 21:50:03 UTC

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Package quickmatch updated to version 0.2.1 with previous version 0.2.0 dated 2018-08-21

Title: Quick Generalized Full Matching
Description: Provides functions for constructing near-optimal generalized full matching. Generalized full matching is an extension of the original full matching method to situations with more intricate study designs. The package is made with large data sets in mind and derives matches more than an order of magnitude quicker than other methods.
Author: Fredrik Savje [aut, cre], Jasjeet Sekhon [aut], Michael Higgins [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between quickmatch versions 0.2.0 dated 2018-08-21 and 0.2.1 dated 2018-08-24

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Package lucid updated to version 1.6 with previous version 1.4 dated 2016-10-24

Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped. See: Wright (2016). Lucid: An R Package for Pretty-Printing Floating Point Numbers. In JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association. 2270-2279.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>

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Package ggthemes updated to version 4.0.1 with previous version 4.0.0 dated 2018-07-19

Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre] (<https://orcid.org/0000-0001-9953-3904>), Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb], Baptise Auguie [ctb], Bob Rudis [ctb], Hadley Wickham [ctb] (Code from the ggplot2 package.), Justin Talbot [ctb] (Code from the labeling package), Joshua London [ctb]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>

Diff between ggthemes versions 4.0.0 dated 2018-07-19 and 4.0.1 dated 2018-08-24

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New package stepPenal with initial version 0.2
Package: stepPenal
Type: Package
Title: Stepwise Forward Variable Selection in Penalized Regression
Version: 0.2
Author: Eleni Vradi
Maintainer: Eleni Vradi <vradi.eleni@gmail.com>
Description: Model Selection Based on Combined Penalties. This package implements a stepwise forward variable selection algorithm based on a penalized likelihood criterion that combines the L0 with L2 or L1 norms.
License: GPL-2
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: glmnet, mvtnorm, pROC, dfoptim, caret, stats, base
NeedsCompilation: no
Encoding: UTF-8
RoxygenNote: 6.1.0
Packaged: 2018-08-24 06:56:09 UTC; vradi
Repository: CRAN
Date/Publication: 2018-08-24 20:50:03 UTC

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New package ncappc with initial version 0.3.0
Package: ncappc
Title: NCA Calculations and Population Model Diagnosis
Version: 0.3.0
Authors@R: c(person("Chayan", "Acharya", role = "aut"), person("Andrew C.", "Hooker", role = c("aut", "cre"), email = "andrew.hooker@farmbio.uu.se"), person("Gulbeyaz Y.", "Turkyilmaz", role = "aut"), person("Siv", "Jonsson", role = "aut"), person("Mats O.", "Karlsson", role = "aut"))
Description: A flexible tool that can perform (i) traditional non-compartmental analysis (NCA) and (ii) Simulation-based posterior predictive checks for population pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using NCA metrics.
Depends: R (>= 2.15.3),
Imports: scales, gtable, knitr, xtable, reshape2, dplyr, Cairo, readr (>= 0.2.2), lazyeval, PopED, magrittr, rlang, purrr, tibble, rmarkdown, tidyr, ggplot2 (>= 2.0.0), grid, gridExtra (>= 2.0.0), grDevices, stats, bookdown
Suggests: testthat
License: GPL-3
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-24 15:58:33 UTC; ancho179
Author: Chayan Acharya [aut], Andrew C. Hooker [aut, cre], Gulbeyaz Y. Turkyilmaz [aut], Siv Jonsson [aut], Mats O. Karlsson [aut]
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>
Repository: CRAN
Date/Publication: 2018-08-24 20:30:03 UTC

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Package incidence updated to version 1.4.1 with previous version 1.3.1 dated 2018-06-11

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

Diff between incidence versions 1.3.1 dated 2018-06-11 and 1.4.1 dated 2018-08-24

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Package CrossVA updated to version 0.9.2 with previous version 0.9.1 dated 2017-09-04

Title: Verbal Autopsy Data Transform for Use with Various Coding Algorithms
Description: Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (Revision 1.4.1) for automated coding of Cause of Death using different computer algorithms. Currently supports user-supplied mappings, and provides unvalidated, experimental-stage mapping definitions to transform to InterVA4, Tariff 2, and InSilicoVA. This package is made available by WHO, in collaboration with Swiss Tropical and Public Health Institute.
Author: Nicolas Maire <nma.swisstph@gmail.com> [aut], Jason Thomas [cre], Eungang Choi, Zehang Li, Sam Clark,
Maintainer: Jason Thomas <jarathomas@gmail.com>

Diff between CrossVA versions 0.9.1 dated 2017-09-04 and 0.9.2 dated 2018-08-24

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Package BGData updated to version 2.0.0 with previous version 1.0.0 dated 2017-05-11

Title: A Suite of Packages for Analysis of Big Genomic Data
Description: An umbrella package providing a phenotype/genotype data structure and scalable and efficient computational methods for large genomic datasets in combination with several other packages: 'BEDMatrix', 'LinkedMatrix', and 'symDMatrix'.
Author: Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre], Paulino Perez [ctb], Ana Vazquez [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>

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Package bacistool updated to version 0.9.8 with previous version 0.9.6 dated 2018-08-09

Title: Bayesian Classification and Information Sharing (BaCIS) Tool for the Design of Multi-Group Phase II Clinical Trials
Description: Provides the design of multi-group phase II clinical trials with binary outcomes using the hierarchical Bayesian classification and information sharing (BaCIS) model. Subgroups are classified into two clusters on the basis of their outcomes mimicking the hypothesis testing framework. Subsequently, information sharing takes place within subgroups in the same cluster, rather than across all subgroups. This method can be applied to the design and analysis of multi-group clinical trials with binary outcomes.
Author: Nan Chen and J. Jack Lee
Maintainer: Nan Chen <nchen2@mdanderson.org>

Diff between bacistool versions 0.9.6 dated 2018-08-09 and 0.9.8 dated 2018-08-24

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Package arrangements updated to version 1.1.2 with previous version 1.1.1 dated 2018-08-22

Title: Fast Generators and Iterators for Permutations, Combinations and Partitions
Description: Fast generators and iterators for permutations, combinations and partitions. The iterators allow users to generate arrangements in a memory efficient manner and the generated arrangements are in lexicographical (dictionary) order. Permutations and combinations can be drawn with/without replacement and support multisets. It has been demonstrated that 'arrangements' outperforms most of the existing packages of similar kind. Some benchmarks could be found at <https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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 src/permutations/k_permutations.h           |    4 ++--
 src/permutations/multiset_permutations.h    |    2 +-
 src/permutations/ordinary_permutations.h    |    2 +-
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Package wordcloud updated to version 2.6 with previous version 2.5 dated 2014-06-12

Title: Word Clouds
Description: Functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.
Author: Ian Fellows
Maintainer: Ian Fellows <ian@fellstat.com>

Diff between wordcloud versions 2.5 dated 2014-06-12 and 2.6 dated 2018-08-24

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Package symDMatrix updated to version 2.0.1 with previous version 2.0.0 dated 2018-08-07

Title: Partitioned Symmetric Matrices
Description: A matrix-like class to represent a symmetric matrix partitioned into file-backed blocks.
Author: Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>

Diff between symDMatrix versions 2.0.0 dated 2018-08-07 and 2.0.1 dated 2018-08-24

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 9 files changed, 31 insertions(+), 19 deletions(-)

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Package NAM updated to version 1.6.2 with previous version 1.6.1 dated 2018-06-28

Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>

Diff between NAM versions 1.6.1 dated 2018-06-28 and 1.6.2 dated 2018-08-24

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Package BMRBr updated to version 0.2.0 with previous version 0.1.0 dated 2018-01-17

Title: 'BMRB' File Downloader
Description: Nuclear magnetic resonance (NMR) is a highly versatile analytical technique for studying molecular configuration, conformation, and dynamics, especially those of biomacromolecules such as proteins. Biological Magnetic Resonance Data Bank ('BMRB') is a repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules. Currently, 'BMRB' offers an R package 'RBMRB' to fetch data, however, it doesn't easily offer individual data file downloading and storing in a local directory. When using 'RBMRB', the data will stored as an R object, which fundamentally hinders the NMR researches to access the rich information from raw data, for example, the metadata. Here, 'BMRBr' File Downloader ('BMRBr') offers a more fundamental, low level downloader, which will download original deposited .str format file. This type of file contains information such as entry title, authors, citation, protein sequences, and so on. Many factors affect NMR experiment outputs, such as temperature, resonance sensitivity and etc., approximately 40% of the entries in the 'BMRB' have chemical shift accuracy problems [1,2] Unfortunately, current reference correction methods are heavily dependent on the availability of assigned protein chemical shifts or protein structure. This is my current research project is going to solve, which will be included in the future release of the package. The current version of the package is sufficient and robust enough for downloading individual 'BMRB' data file from the 'BMRB' database <http://www.bmrb.wisc.edu>. The functionalities of this package includes but not limited: * To simplifies NMR researches by combine data downloading and results analysis together. * To allows NMR data reaches a broader audience that could utilize more than just chemical shifts but also metadata. * To offer reference corrected data for entries without assignment or structure information (future release). Reference: [1] E.L. Ulrich, H. Akutsu, J.F. Doreleijers, Y. Harano, Y.E. Ioannidis, J. Lin, et al., BioMagResBank, Nucl. Acids Res. 36 (2008) D402–8. <doi:10.1093/nar/gkm957>. [2] L. Wang, H.R. Eghbalnia, A. Bahrami, J.L. Markley, Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications, J. Biomol. NMR. 32 (2005) 13–22. <doi:10.1007/s10858-005-1717-0>.
Author: Xi Chen [aut, cre] (<https://orcid.org/0000-0001-7094-6748>)
Maintainer: Xi Chen <billchenxi@gmail.com>

Diff between BMRBr versions 0.1.0 dated 2018-01-17 and 0.2.0 dated 2018-08-24

 DESCRIPTION            |   10 -
 MD5                    |   10 -
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 6 files changed, 269 insertions(+), 60 deletions(-)

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New package RTest with initial version 1.1.8.0
Package: RTest
Version: 1.1.8.0
Date: 2018-08-22
Title: A XML-Based Testing Framework for Automated Component Tests of R Packages
Authors@R: c( person("Sebastian", "Wolf", , "sebastian.wolf.sw1@roche.com", role = c("aut","cre")), person("Matthias", "Pfeifer", , "matthias.pfeifer@roche.com", role = c("aut", "ctb")), person("Sergej", "Potapov", , "sergej.potapov@roche.com", role = c("ctb")), person("Roche", role = c("cph", "fnd")) )
Depends: R (>= 3.1.3), testthat (>= 1.0.0), methods
Imports: XML, base64, jsonlite, stringr
Suggests: knitr, rmarkdown
Description: This provides a framework for R packages developed for a regulatory environment. It is based on the 'testthat' unit testing system and provides the adapter functionalities for XML-based test case definition as well as for standardized reporting of the test results.
Collate: RTest-package.R utils.R utils.test.R utils.xmlRead.R utils.xmlWrite.R RTestCollection.R RTestCase.R RTestCase.test-adapter.R
SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or libmagick++-dev (deb)
VignetteBuilder: knitr
License: GPL (>= 2)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-22 14:31:04 UTC; wolfs25
Author: Sebastian Wolf [aut, cre], Matthias Pfeifer [aut, ctb], Sergej Potapov [ctb], Roche [cph, fnd]
Maintainer: Sebastian Wolf <sebastian.wolf.sw1@roche.com>
Repository: CRAN
Date/Publication: 2018-08-24 16:54:27 UTC

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New package roperators with initial version 1.0.1
Package: roperators
Type: Package
Title: Additional Operators to Help you Write Cleaner R Code
Version: 1.0.1
Maintainer: Ben Wiseman <benjamin.wiseman@kornferry.com>
Authors@R: c(person('Ben', 'Wiseman', role = c('cre', 'aut', 'ccp'), email = 'benjamin.wiseman@kornferry.com'), person('Steven', 'Nydick', role = c('aut', 'ccp'), email = 'steven.nydick@kornferry.com'), person('Jeff', 'Jones', role = c('aut', 'led'), email = 'jeff.jones@kornferry.com'))
Description: Provides string arithmetic, reassignment operators, logical operators that handle missing values, and extra logical operators such as floating point equality and all or nothing. The intent is to allow R users to write code that is easier to read, write, and maintain while providing a friendlier experience to new R users from other language backgrounds (such as 'Python') who are used to concepts such as x += 1 and 'foo' + 'bar'.
Encoding: UTF-8
LazyData: true
Copyright: Korn Ferry International
License: MIT + file LICENSE
RoxygenNote: 6.1.0
Suggests: magrittr
Collate: 'type_checks.R' 'operators.R' 'shorthand.R' 'write_pdf.R'
NeedsCompilation: no
Packaged: 2018-08-21 15:09:41 UTC; benwiseman
Author: Ben Wiseman [cre, aut, ccp], Steven Nydick [aut, ccp], Jeff Jones [aut, led]
Repository: CRAN
Date/Publication: 2018-08-24 16:40:03 UTC

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New package portfolio.optimization with initial version 1.0-0
Package: portfolio.optimization
Type: Package
Title: Contemporary Portfolio Optimization
Version: 1.0-0
Date: 2018-08-20
Authors@R: c( person("Ronald", "Hochreiter", email = "ron@hochreiter.net", role = c("aut", "cre")))
Maintainer: Ronald Hochreiter <ron@hochreiter.net>
Description: Simplify your portfolio optimization process by applying a contemporary modeling way to model and solve your portfolio problems. While most approaches and packages are rather complicated this one tries to simplify things and is agnostic regarding risk measures as well as optimization solvers. Some of the methods implemented are described by Konno and Yamazaki (1991) <doi:10.1287/mnsc.37.5.519>, Rockafellar and Uryasev (2001) <doi:10.21314/JOR.2000.038> and Markowitz (1952) <doi:10.1111/j.1540-6261.1952.tb01525.x>.
Depends: R (>= 3.5), xts, MASS, magrittr, modopt.matlab
License: MIT + file LICENSE
URL: http://www.finance-r.com/
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-20 16:51:33 UTC; ron
Author: Ronald Hochreiter [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-24 16:10:18 UTC

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Package perccalc updated to version 1.0.3 with previous version 1.0.2 dated 2018-07-18

Title: Estimate Percentiles from an Ordered Categorical Variable
Description: An implementation of two functions that estimate values for percentiles from an ordered categorical variable as described by Reardon (2011, isbn:978-0-87154-372-1). One function estimates percentile differences from two percentiles while the other returns the values for every percentile from 1 to 100.
Author: Jorge Cimentada [aut, cre]
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>

Diff between perccalc versions 1.0.2 dated 2018-07-18 and 1.0.3 dated 2018-08-24

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 MD5                                   |   22 ++--
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 inst/doc/perc_warning_example.R       |    1 
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 12 files changed, 225 insertions(+), 234 deletions(-)

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New package MRFcov with initial version 1.0.35
Package: MRFcov
Type: Package
Title: Markov Random Fields with Additional Covariates
Version: 1.0.35
Date/Publication: 2018-08-24 16:24:34 UTC
URL: https://github.com/nicholasjclark/MRFcov
Authors@R: c( person("Nicholas J", "Clark", email = "nicholas.j.clark1214@gmail.com", role = c("aut", "cre")), person("Konstans", "Wells", email = "konswells@gmail.com", role = "aut"), person("Oscar", "Lindberg", email = "o.lindberg@gmail.com", role = "aut"))
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Description: Approximate node interaction parameters of Markov Random Fields graphical networks. Models can incorporate additional covariates, allowing users to estimate how interactions between nodes in the graph are predicted to change across covariate gradients. The general methods implemented in this package are described in Clark et al. (2018) <doi:10.1002/ecy.2221>.
Depends: R (>= 3.3.3), glmnet
Imports: purrr, parallel, plyr, ggplot2, dplyr, caret, gridExtra, magrittr, Matrix, stats, utils, reshape2, sfsmisc, igraph, grDevices, pbapply, mgcv
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.0.1
LazyData: true
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-20 23:03:32 UTC; nicholasclark
Author: Nicholas J Clark [aut, cre], Konstans Wells [aut], Oscar Lindberg [aut]
Repository: CRAN

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New package krige with initial version 0.1-1
Package: krige
Version: 0.1-1
Date: 2018-08-14
Title: Geospatial Kriging with Metropolis Sampling
Author: Jason S. Byers [aut, cre], Jeff Gill [aut], James E. Monogan III [aut]
Maintainer: Jason S. Byers <byersjs@uga.edu>
Depends: R (>= 2.10), mvtnorm, MASS
Description: Estimates kriging models for geographical point-referenced data. Method is described in Monogan and Gill (2016) <doi:10.1017/psrm.2015.5>.
License: GPL (>= 2)
LazyData: true
URL: https://www.r-project.org
Packaged: 2018-08-21 02:31:20 UTC; monogan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-08-24 16:22:18 UTC
RoxygenNote: 6.1.0

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Package gmvarkit updated to version 1.0.2 with previous version 1.0.1 dated 2018-08-13

Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Maximum likelihood estimation of Gaussian Mixture Vector Autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics, forecasting and simulations. Applying general linear constraints to the autoregressive parameters is supported. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>

Diff between gmvarkit versions 1.0.1 dated 2018-08-13 and 1.0.2 dated 2018-08-24

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Package dr4pl updated to version 1.1.6 with previous version 1.1.1 dated 2018-03-21

Title: Dose Response Data Analysis using the 4 Parameter Logistic (4pl) Model
Description: Models the relationship between dose levels and responses in a pharmacological experiment using the 4 Parameter Logistic model. Traditional packages on dose-response modelling such as 'drc' and 'nplr' often draw errors due to convergence failure especially when data have outliers or non-logistic shapes. This package provides robust estimation methods that are less affected by outliers and other initialization methods that work well for data lacking logistic shapes. We provide the bounds on the parameters of the 4PL model that prevent parameter estimates from diverging or converging to zero and base their justification in a statistical principle. These methods are used as remedies to convergence failure problems. Gadagkar, S. R. and Call, G. B. (2015) <doi:10.1016/j.vascn.2014.08.006> Ritz, C. and Baty, F. and Streibig, J. C. and Gerhard, D. (2015) <doi:10.1371/journal.pone.0146021>.
Author: Justin T. Landis [aut, cre], Hyowon An [aut], Aubrey G. Bailey [aut]
Maintainer: Justin T. Landis <jtlandis314@gmail.com>

Diff between dr4pl versions 1.1.1 dated 2018-03-21 and 1.1.6 dated 2018-08-24

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 18 files changed, 850 insertions(+), 378 deletions(-)

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New package xRing with initial version 0.1.0
Package: xRing
Type: Package
Title: Visualization and Correction of X-Ray Micro-Density Profiles
Version: 0.1.0
Author: Filipe Campelo and Konrad Mayer
Maintainer: Filipe Campelo <fcampelo@ci.uc.pt>
Description: Contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface to visualize density profiles and correct tree-ring borders.
Depends: R (>= 3.3)
Suggests: detrendeR
Imports: dplR, imager, tcltk2, tkRplotR
License: GPL (>= 2)
ByteCompile: yes
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-20 14:51:43 UTC; filipe
Repository: CRAN
Date/Publication: 2018-08-24 15:50:02 UTC

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New package tidytidbits with initial version 0.1.0
Package: tidytidbits
Type: Package
Title: A Collection of Tools and Helpers Extending the Tidyverse
Version: 0.1.0
Author: Marcel Wiesweg [aut, cre]
Maintainer: Marcel Wiesweg <marcel.wiesweg@uk-essen.de>
Authors@R: person("Marcel", "Wiesweg", email = "marcel.wiesweg@uk-essen.de", role = c("aut", "cre"))
Description: A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages. This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of 'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count, various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks, saving to PDF and PNG from a pipe and various small utilities.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: utils, stats, grDevices, methods, dplyr, forcats, grid, purrr, stringr, tibble, tidyr, tidyselect, extrafont, rlang, magrittr
Suggests: survival
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-20 12:27:39 UTC; wiesweg
Repository: CRAN
Date/Publication: 2018-08-24 15:50:07 UTC

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New package survxai with initial version 0.2.0
Package: survxai
Title: Visualization of the Local and Global Survival Model Explanations
Version: 0.2.0
Authors@R: c( person("Aleksandra", "Grudziaz", email = "aleksandra.grudziaz@gmail.com", role = c("aut", "cre")), person("Alicja", "Gosiewska", email = "alicjagosiewska@gmail.com", role = c("aut")), person("Przemyslaw", "Biecek", email = "przemyslaw.biecek@gmail.com", role = c("aut", "ths")) )
Description: Survival models may have very different structures. This package contains functions for creating a unified representation of a survival models, which can be further processed by various survival explainers. Tools implemented in 'survxai' help to understand how input variables are used in the model and what impact do they have on the final model prediction. Currently, four explanation methods are implemented. We can divide them into two groups: local and global.
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: breakDown, ggplot2, pec, scales, survival, survminer
Depends: prodlim
Suggests: CFC, covr, knitr, randomForestSRC, rmarkdown, rms, testthat, tibble
VignetteBuilder: knitr
URL: https://mi2datalab.github.io/survxai/
BugReports: https://github.com/MI2DataLab/survxai/issues
NeedsCompilation: no
Packaged: 2018-08-20 12:34:05 UTC; Aleksandra Grudziaz
Author: Aleksandra Grudziaz [aut, cre], Alicja Gosiewska [aut], Przemyslaw Biecek [aut, ths]
Maintainer: Aleksandra Grudziaz <aleksandra.grudziaz@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-24 15:50:12 UTC

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Package RcmdrPlugin.NMBU updated to version 1.8.9 with previous version 1.8.8 dated 2018-01-03

Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between RcmdrPlugin.NMBU versions 1.8.8 dated 2018-01-03 and 1.8.9 dated 2018-08-24

 DESCRIPTION                     |    8 ++++----
 MD5                             |    5 +++--
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 4 files changed, 8 insertions(+), 6 deletions(-)

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Package iotables updated to version 0.3.1 with previous version 0.2.9 dated 2018-08-05

Title: Importing and Manipulating Symmetric Input-Output Tables
Description: Pre-processing tasks related to working with Eurostat's symmetric input-output tables and provide basic input-output economics calculations. The package is a part of rOpenGov <http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal
Maintainer: Daniel Antal <daniel.antal@ceemid.eu>

Diff between iotables versions 0.2.9 dated 2018-08-05 and 0.3.1 dated 2018-08-24

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Package bamdit updated to version 3.2.0 with previous version 3.1.0 dated 2017-05-31

Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Functions for Bayesian meta-analysis of diagnostic test data which are based on a scale mixtures bivariate random-effects model.
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>

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Package scclust updated to version 0.2.0 with previous version 0.1.2 dated 2018-07-21

Title: Size-Constrained Clustering
Description: Provides wrappers for 'scclust', a C library for computationally efficient size-constrained clustering with near-optimal performance. See <https://github.com/fsavje/scclust> for more information.
Author: Fredrik Savje [aut, cre], Michael Higgins [aut], Jasjeet Sekhon [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

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Package robeth updated to version 2.7-4 with previous version 2.7-2 dated 2018-06-13

Title: R Functions for Robust Statistics
Description: Locations problems, M-estimates of coefficients and scale in linear regression, Weights for bounded influence regression, Covariance matrix of the coefficient estimates, Asymptotic relative efficiency of regression M-estimates, Robust testing in linear models, High breakdown point regression, M-estimates of covariance matrices, M-estimates for discrete generalized linear models.
Author: Alfio Marazzi <Alfio.Marazzi@chuv.ch>
Maintainer: A. Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>

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Package REAT updated to version 2.0.1 with previous version 2.0.0 dated 2018-03-27

Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>

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Package polymapR updated to version 1.0.17 with previous version 1.0.15 dated 2018-04-13

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

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Package MoEClust updated to version 1.2.0 with previous version 1.1.0 dated 2018-02-06

Title: Gaussian Parsimonious Clustering Models with Covariates
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2017) <arXiv:1711.05632>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations via the EM algorithm. Visualisation of the results of such models using generalised pairs plots is also facilitated.
Author: Keefe Murphy [aut, cre], Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>

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Package iC10TrainingData updated to version 1.3.1 with previous version 1.0.1 dated 2014-09-26

Title: Training Datasets for iC10 Package
Description: Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
Author: Oscar M Rueda and Jose Antonio Seoane Fernandez
Maintainer: Oscar M. Rueda <Oscar.Rueda@cruk.cam.ac.uk>

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Package BiocManager updated to version 1.30.2 with previous version 1.30.1 dated 2018-06-15

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>

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Package xergm updated to version 1.8.3 with previous version 1.8.2 dated 2017-04-02

Title: Extensions of Exponential Random Graph Models
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), Temporal Network Autocorrelation Models (TNAM), and Relational Event Models (REM). This package acts as a meta-package for several sub-packages on which it depends.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [aut], Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>

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Package adiv updated to version 1.2 with previous version 1.1 dated 2017-09-14

Title: Analysis of Diversity
Description: Includes functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. It also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>

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New package optiSel with initial version 2.0.2
Package: optiSel
Type: Package
Title: Optimum Contribution Selection and Population Genetics
Version: 2.0.2
Date: 2018-08-24
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Depends: R (>= 3.5.0)
Description: A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
License: GPL-2
Imports: Matrix, plyr, kinship2, nadiv, pedigree, pspline, stringr, MASS, methods, stats, purrr, graphics, quadprog, data.table, magic, parallel, doParallel, foreach, ECOSolveR, reshape2, optiSolve, Rcpp (>= 0.12.4)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, ggplot2, rmarkdown
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-08-24 11:15:30 UTC; Robin
Repository: CRAN
Date/Publication: 2018-08-24 12:20:02 UTC

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Package littler updated to version 0.3.4 with previous version 0.3.3 dated 2017-12-17

Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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New package twl with initial version 1.0
Package: twl
Type: Package
Title: Two-Way Latent Structure Clustering Model
Version: 1.0
Date: 2018-08-17
Author: Michael Swanson
Maintainer: Michael Swanson <dms866@mail.harvard.edu>
Description: Implementation of a Bayesian two-way latent structure model for integrative genomic clustering. The model clusters samples in relation to distinct data sources, with each subject-dataset receiving a latent cluster label, though cluster labels have across-dataset meaning because of the model formulation. A common scaling across data sources is unneeded, and inference is obtained by a Gibbs Sampler. The model can fit multivariate Gaussian distributed clusters or a heavier-tailed modification of a Gaussian density. Uniquely among integrative clustering models, the formulation makes no nestedness assumptions of samples across data sources -- the user can still fit the model if a study subject only has information from one data source. The package provides a variety of post-processing functions for model examination including ones for quantifying observed alignment of clusterings across genomic data sources. Run time is optimized so that analyses of datasets on the order of thousands of features on fewer than 5 datasets and hundreds of subjects can converge in 1 or 2 days on a single CPU. See "Swanson DM, Lien T, Bergholtz H, Sorlie T, Frigessi A, Investigating Coordinated Architectures Across Clusters in Integrative Studies: a Bayesian Two-Way Latent Structure Model, 2018, <doi:10.1101/387076>, Cold Spring Harbor Laboratory" at <https://www.biorxiv.org/content/early/2018/08/07/387076.full.pdf> for model details.
License: GPL (>= 2)
Imports: Rfast
Depends: R (>= 2.10), data.table, MCMCpack, corrplot
RoxygenNote: 6.0.1
LazyData: true
NeedsCompilation: no
Packaged: 2018-08-17 10:41:22 UTC; davidswanson
Repository: CRAN
Date/Publication: 2018-08-24 11:00:03 UTC

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Package keras updated to version 2.2.0 with previous version 2.1.6 dated 2018-04-29

Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: JJ Allaire [aut, cre], François Chollet [aut, cph], RStudio [ctb, cph, fnd], Google [ctb, cph, fnd], Yuan Tang [ctb, cph] (<https://orcid.org/0000-0001-5243-233X>), Daniel Falbel [ctb, cph], Wouter Van Der Bijl [ctb, cph], Martin Studer [ctb, cph]
Maintainer: JJ Allaire <jj@rstudio.com>

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Package binGroup updated to version 2.2-1 with previous version 2.1-1 dated 2018-03-16

Title: Evaluation and Experimental Design for Binomial Group Testing
Description: Methods for estimation and hypothesis testing of proportions in group testing designs: methods for estimating a proportion in a single population (assuming sensitivity and specificity equal to 1 in designs with equal group sizes), as well as hypothesis tests and functions for experimental design for this situation. For estimating one proportion or the difference of proportions, a number of confidence interval methods are included, which can deal with various different pool sizes. Further, regression methods are implemented for simple pooling and matrix pooling designs. Methods for identification of positive items in group testing designs: Optimal testing configurations can be found for hierarchical and array-based algorithms. Operating characteristics can be calculated for testing configurations across a wide variety of situations.
Author: Boan Zhang [aut], Christopher Bilder [aut], Brad Biggerstaff [aut], Frank Schaarschmidt [aut, cre], Brianna Hitt [aut]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>

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Package rtrim updated to version 2.0.6 with previous version 2.0.5 dated 2018-08-16

Title: Trends and Indices for Monitoring Data
Description: The TRIM model is widely used for estimating growth and decline of animal populations based on (possibly sparsely available) count data. The current package is a reimplementation of the original TRIM software developed at Statistics Netherlands by Jeroen Pannekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d> for more information about TRIM.
Author: Patrick Bogaart [aut, cre], Mark van der Loo [aut], Jeroen Pannekoek [aut]
Maintainer: Patrick Bogaart <rtrim@cbs.nl>

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Package callr updated to version 3.0.0 with previous version 2.0.4 dated 2018-05-15

Title: Call R from R
Description: It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>), Winston Chang [aut], RStudio [cph, fnd], Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package BGLR updated to version 1.0.7 with previous version 1.0.5.1 dated 2018-08-21

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>

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Package STMotif updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-07

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 depmixS4 updated to version 1.3-5 with previous version 1.3-3 dated 2016-02-15

Title: Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4
Description: Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models.
Author: Ingmar Visser <i.visser@uva.nl>, Maarten Speekenbrink <m.speekenbrink@ucl.ac.uk>
Maintainer: Ingmar Visser <i.visser@uva.nl>

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Package accelerometry updated to version 3.1.2 with previous version 3.1.1 dated 2018-08-21

Title: Functions for Processing Accelerometer Data
Description: A collection of functions that perform operations on time-series accelerometer data, such as identify non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented. Most of the functions are written in C++ for efficiency.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>

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Package plsgenomics updated to version 1.5-2 with previous version 1.5-1 dated 2017-09-14

Title: PLS Analyses for Genomics
Description: Routines for PLS-based genomic analyses, implementing PLS methods for classification with microarray data and prediction of transcription factor activities from combined ChIP-chip analysis. The >=1.2-1 versions include two new classification methods for microarray data: GSIM and Ridge PLS. The >=1.3 versions includes a new classification method combining variable selection and compression in logistic regression context: logit-SPLS; and an adaptive version of the sparse PLS.
Author: Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>, Ghislain Durif <gd.dev@libertymail.net>, Sophie Lambert-Lacroix <sophie.lambert-lacroix@univ-grenoble-alpes.fr>, Julie Peyre <Julie.Peyre@univ-grenoble-alpes.fr>, and Korbinian Strimmer <k.strimmer@imperial.ac.uk>.
Maintainer: Ghislain Durif <gd.dev@libertymail.net>

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Package mvglmmRank updated to version 1.2-2 with previous version 1.2-1 dated 2018-04-19

Title: Multivariate Generalized Linear Mixed Models for Ranking Sports Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation.
Author: Andrew T. Karl (Adsurgo LLC), Jennifer Broatch (Arizona State University)
Maintainer: Andrew T. Karl <akarl@asu.edu>

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Package btergm updated to version 1.9.3 with previous version 1.9.1 dated 2018-02-15

Title: Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb], Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>

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