Mon, 26 Jun 2017

Package BatchGetSymbols updated to version 1.2 with previous version 1.1 dated 2016-12-05

Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo or Google Finance.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between BatchGetSymbols versions 1.1 dated 2016-12-05 and 1.2 dated 2017-06-26

 DESCRIPTION                            |   10 
 MD5                                    |   26 +-
 NEWS.md                                |    4 
 R/BatchGetSymbols.R                    |  328 +++++++++++++++----------------
 R/GetSP500Stocks.R                     |   60 ++---
 R/OnAttach.R                           |    1 
 build/vignette.rds                     |binary
 inst/doc/BatchGetSymbols-vignette.R    |   84 ++++----
 inst/doc/BatchGetSymbols-vignette.Rmd  |  164 +++++++--------
 inst/doc/BatchGetSymbols-vignette.html |  343 ++++++++++++++++-----------------
 man/BatchGetSymbols.Rd                 |  108 +++++-----
 man/GetSP500Stocks.Rd                  |    3 
 man/myGetSymbols.Rd                    |    1 
 vignettes/BatchGetSymbols-vignette.Rmd |  164 +++++++--------
 14 files changed, 648 insertions(+), 648 deletions(-)

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Package sqlscore updated to version 0.1.2 with previous version 0.1.1 dated 2017-01-07

Title: Utilities for Generating SQL Queries from Model Objects
Description: Provides utilities for generating SQL queries (particularly CREATE TABLE statements) from R model objects. The most important use case is generating SQL to score a generalized linear model or related model represented as an R object, in which case the package handles parsing formula operators and including the model's response function.
Author: William Brannon [aut, cre]
Maintainer: William Brannon <wwbrannon@email.wm.edu>

Diff between sqlscore versions 0.1.1 dated 2017-01-07 and 0.1.2 dated 2017-06-26

 DESCRIPTION                            |   10 -
 LICENSE                                |    2 
 MD5                                    |   45 +++----
 NAMESPACE                              |   12 -
 NEWS.md                                |    6 
 R/extract_coef.R                       |   34 ++---
 R/extract_factors.R                    |   22 +--
 R/linkfun.R                            |only
 R/score_expression.R                   |  208 ++-------------------------------
 R/sqlscore.R                           |  127 ++++++++++----------
 R/utils.R                              |   47 ++++++-
 README.md                              |    2 
 man/create_statement.Rd                |    6 
 man/linpred.Rd                         |    2 
 man/score_expression.Rd                |   22 ---
 man/select_statement.Rd                |    6 
 man/sqlscore.Rd                        |    2 
 tests/testthat/helper-functions.R      |    2 
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 tests/testthat/test-extract_factors.R  |   12 -
 tests/testthat/test-extract_offsets.R  |   14 +-
 tests/testthat/test-fqtn.R             |   15 +-
 tests/testthat/test-score_expression.R |   14 +-
 24 files changed, 258 insertions(+), 398 deletions(-)

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New package rattle.data with initial version 1.0.2
Package: rattle.data
Title: Rattle Datasets
Version: 1.0.2
Date: 2017-06-26
Author: Graham Williams
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Description: Contains the datasets used as default examples by the rattle package. The datasets themselves can be used independently of the rattle package to illustrate analytics, data mining, and data science tasks.
Depends: R (>= 2.10)
Suggests: rattle
LazyData: yes
License: GPL-3
NeedsCompilation: no
Repository: CRAN
Packaged: 2017-06-26 04:12:47 UTC; gjw
Date/Publication: 2017-06-26 06:12:10 UTC

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New package helixvis with initial version 0.1.0
Package: helixvis
Type: Package
Title: Visualize Alpha-Helical Peptide Sequences
Date: 2017-06-19
Version: 0.1.0
Authors@R: c( person("Raoul", "Wadhwa", email = "raoulwadhwa@gmail.com", role = c("cre", "aut")), person("Regina", "Stevens-Truss", email = "rtruss@kzoo.edu", role = "aut"))
Description: Create pretty visualizations of alpha-helical peptide sequences in R. The amino acid type (polar, hydrophobic, etc.) is denoted by color. This package allows creation of helical wheels, and the newer Wenxiang diagrams. Future versions aim to include increased customizability of the two existing visualizations, as well as a visualization for the helical net diagram.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: rJava (>= 0.9)
Depends: R (>= 3.2.5)
SystemRequirements: Java JDK 1.8 or higher
URL: https://github.com/rrrlw/helixvis
BugReports: https://github.com/rrrlw/helixvis/issues
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-06-26 01:10:15 UTC; raoul
Author: Raoul Wadhwa [cre, aut], Regina Stevens-Truss [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-26 06:13:24 UTC

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Package getCRUCLdata updated to version 0.1.7 with previous version 0.1.6 dated 2017-06-13

Title: Use and Explore CRU CL v. 2.0 Climatology Elements in R
Description: Provides functions that automate downloading and importing University of East Anglia Climate Research Unit (CRU) CL v. 2.0 climatology data into R, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a tidy data frame as a tibble or a list of raster stack objects for use in an R session. CRU CL v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arcminutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (http://orcid.org/0000-0002-0061-8359)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

Diff between getCRUCLdata versions 0.1.6 dated 2017-06-13 and 0.1.7 dated 2017-06-26

 DESCRIPTION                            |   10 ++++----
 MD5                                    |   38 +++++++++++++++++----------------
 NEWS.md                                |   13 +++++++++++
 R/get_CRU.R                            |    9 +++----
 R/get_CRU_df.R                         |    9 -------
 R/get_CRU_stack.R                      |    9 -------
 R/manage_cached_files.R                |   16 ++++++-------
 R/set_cache.R                          |only
 README.md                              |   15 ++++++-------
 inst/doc/getCRUCLdata.R                |    4 +--
 inst/doc/getCRUCLdata.Rmd              |    4 +--
 inst/doc/getCRUCLdata.html             |    4 +--
 tests/testthat/test-create_CRU_df.R    |    4 +--
 tests/testthat/test-create_CRU_stack.R |    4 +--
 tests/testthat/test-create_df.R        |    6 ++---
 tests/testthat/test-create_stack.R     |   10 ++++----
 tests/testthat/test-get_CRU_df.R       |    4 +--
 tests/testthat/test-get_CRU_stack.R    |    4 +--
 tests/testthat/test_get_local.R        |    4 +--
 tests/testthat/test_set_cache.R        |only
 vignettes/getCRUCLdata.Rmd             |    4 +--
 21 files changed, 85 insertions(+), 86 deletions(-)

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New package easyml with initial version 0.1.0
Package: easyml
Version: 0.1.0
Title: Easily Build and Evaluate Machine Learning Models
Description: Easily build and evaluate machine learning models on a dataset. Machine learning models supported include penalized linear models, penalized linear models with interactions, random forest, support vector machines, neural networks, and deep neural networks.
Authors@R: c( person("Woo-Young", "Ahn", , "ahn.280@osu.edu", c("aut", "cre")), person("Paul", "Hendricks", , "paul.hendricks.2013@owu.edu", "aut"), person("OSU-CCSL", role = "cph"))
License: MIT + file LICENSE
LazyData: true
Depends: R (>= 3.3.1)
Imports: caret, corrplot, darch, dummies, e1071, futile.logger, ggplot2, glinternet, glmnet, parallel, pbapply, pbmcapply, pROC, nnet, randomForest, scales, scorer
Suggests: covr, lintr, testthat, knitr, rmarkdown
URL: https://github.com/CCS-Lab/easyml
BugReports: https://github.com/CCS-Lab/easyml/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-26 00:34:41 UTC; paulhendricks
Author: Woo-Young Ahn [aut, cre], Paul Hendricks [aut], OSU-CCSL [cph]
Maintainer: Woo-Young Ahn <ahn.280@osu.edu>
Repository: CRAN
Date/Publication: 2017-06-26 06:13:47 UTC

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Sun, 25 Jun 2017

New package cytometree with initial version 1.0.0
Package: cytometree
Type: Package
Title: Automated Cytometry Gating
Version: 1.0.0
Date: 2017-06-25
Author: Alkhassim Chariff
Maintainer: Alkhassim Chariff <chariff.alkhassim@gmail.com>
LinkingTo: Rcpp, RcppArmadillo
Description: Given the hypothesis of a bimodal distribution of cells for each marker, the algorithm constructs a binary tree, the nodes of which are subpopulations of cells. At each node, observed cells and markers are modeled by both a family of normal distributions and a family of bimodal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families.
License: LGPL-3 | file LICENSE
LazyData: true
Depends: R (>= 3.1.0), Rcpp (>= 0.12.4)
Imports: ggplot2, graphics, igraph, mclust, stats
RoxygenNote: 6.0.1
BugReports: https://github.com/chariff/Cytometree/issues
NeedsCompilation: yes
Packaged: 2017-06-25 17:07:32 UTC; Chariff
Repository: CRAN
Date/Publication: 2017-06-25 23:01:39 UTC

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New package tidygenomics with initial version 0.1.0
Package: tidygenomics
Type: Package
Title: Tidy Verbs for Dealing with Genomic Data Frames
Version: 0.1.0
Authors@R: c(person("Constantin", "Ahlmann-Eltze", email = "artjom31415@googlemail.com", role = c("aut", "cre")), person("Stan Developers", role="cph", comment="Code from the Stan Math library is reused in 'cluster_interval.cpp'"), person("David", "Robinson", role="cph", comment="Code from the fuzzyjoin package is reused"))
Description: Handle genomic data within data frames just as you would with 'GRanges'. This packages provides method to deal with genomic intervals the "tidy-way" which makes it simpler to integrate in the the general data munging process. The API is inspired by the popular 'bedtools' and the genome_join() method from the 'fuzzyjoin' package.
URL: https://github.com/const-ae/tidygenomics
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, purrr, tidyr, fuzzyjoin (>= 0.1.3), IRanges, Rcpp
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-06-25 18:05:17 UTC; constantin
Author: Constantin Ahlmann-Eltze [aut, cre], Stan Developers [cph] (Code from the Stan Math library is reused in 'cluster_interval.cpp'), David Robinson [cph] (Code from the fuzzyjoin package is reused)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Repository: CRAN
Date/Publication: 2017-06-25 22:45:04 UTC

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Package sitmo updated to version 1.2.0 with previous version 1.1.0 dated 2017-04-28

Title: Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files
Description: Provided within is a high quality and fast PPRNG that is able to be used in an 'OpenMP' parallel environment compiled under either C++98 or C++11. The objective of this package release is to consolidate the distribution of the 'sitmo' library on CRAN by enabling others to link to the 'sitmo' header file instead of including a copy of 'sitmo' within their individual package. Lastly, the package contains example implementations using 'sitmo' and three accompanying vignette that provide additional information.
Author: James Balamuta [aut, cre, cph], Thijs van den Berg [aut, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>

Diff between sitmo versions 1.1.0 dated 2017-04-28 and 1.2.0 dated 2017-06-25

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 sitmo-1.2.0/sitmo/DESCRIPTION                          |   16 
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 sitmo-1.2.0/sitmo/NEWS.md                              |   17 
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 sitmo-1.2.0/sitmo/man/runif_sitmo.Rd                   |    2 
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 sitmo-1.2.0/sitmo/src/RcppExports.cpp                  |   16 
 sitmo-1.2.0/sitmo/src/sitmo_runif.cpp                  |    2 
 sitmo-1.2.0/sitmo/vignettes/sitmo_internals.Rmd        |   50 
 sitmo-1.2.0/sitmo/vignettes/uniform_rng_with_sitmo.Rmd |   18 
 20 files changed, 276 insertions(+), 4137 deletions(-)

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Package PowerNormal updated to version 1.1.0 with previous version 1.0.0 dated 2017-06-04

Title: Power Normal Distribution
Description: Miscellaneous functions for a descriptive analysis and initial inference for the power parameter of the the Power Normal (PN) distribution. This miscellaneous will be extend for more distributions into the power family and the three-parameter model.
Author: Gualberto Segundo Agamez Montalvo, Marcia D'Elia Branco
Maintainer: Gualberto Segundo Agamez Montalvo <gsagamez@gmail.com>

Diff between PowerNormal versions 1.0.0 dated 2017-06-04 and 1.1.0 dated 2017-06-25

 DESCRIPTION     |    6 +++---
 MD5             |   24 ++++++++++++------------
 NAMESPACE       |   14 ++++++++++++--
 R/GerarPN.R     |    2 +-
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 R/biespn.R      |   10 ++++------
 R/densitypn.R   |    4 ++--
 R/estimatepn.R  |    2 +-
 R/histogrampn.R |    2 +-
 R/linespn.R     |    4 ++--
 R/utils.R       |    4 ++--
 man/pn.CI.Rd    |    8 +++-----
 man/pn.bias.Rd  |    7 +++----
 13 files changed, 50 insertions(+), 47 deletions(-)

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Package tensorflow updated to version 0.9 with previous version 0.8.1 dated 2017-05-25

Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
Author: JJ Allaire [aut, cre], RStudio [cph, fnd], Yuan Tang [aut, cph], Dirk Eddelbuettel [ctb, cph], Nick Golding [ctb, cph], Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between tensorflow versions 0.8.1 dated 2017-05-25 and 0.9 dated 2017-06-25

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 9 files changed, 57 insertions(+), 31 deletions(-)

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Package usdm updated to version 1.1-18 with previous version 1.1-15 dated 2015-08-01

Title: Uncertainty Analysis for Species Distribution Models
Description: This is a framework that aims to provide methods and tools for assessing the impact of different sources of uncertainties (e.g.positional uncertainty) on performance of species distribution models (SDMs).)
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between usdm versions 1.1-15 dated 2015-08-01 and 1.1-18 dated 2017-06-25

 DESCRIPTION         |   12 -
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 11 files changed, 736 insertions(+), 683 deletions(-)

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Package TPEA updated to version 3.1.0 with previous version 3.0.1 dated 2017-06-14

Title: A Novel Topology-Based Pathway Enrichment Analysis Approach
Description: We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
Author: Wei Jiang
Maintainer: Wei Jiang <jiangwei@hrbmu.edu.cn>

Diff between TPEA versions 3.0.1 dated 2017-06-14 and 3.1.0 dated 2017-06-25

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 TPEA-3.1.0/TPEA/R/AUEC.R                     |    2 +-
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 TPEA-3.1.0/TPEA/man/num_node_gene_score.Rd   |    2 +-
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Package TAM updated to version 2.3-18 with previous version 2.2-49 dated 2017-06-17

Title: Test Analysis Modules
Description: Includes marginal maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models) and joint maximum likelihood estimation for models from the Rasch family. Latent regression models and plausible value imputation are also supported.
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between TAM versions 2.2-49 dated 2017-06-17 and 2.3-18 dated 2017-06-25

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 NAMESPACE                                             |    5 
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Package PubMedWordcloud updated to version 0.3.4 with previous version 0.3.3 dated 2017-01-16

Title: 'Pubmed' Word Clouds
Description: Create a word cloud using the abstract of publications from 'Pubmed'.
Author: Felix Yanhui Fan <nolanfyh@gmail.com>
Maintainer: Felix Yanhui Fan <nolanfyh@gmail.com>

Diff between PubMedWordcloud versions 0.3.3 dated 2017-01-16 and 0.3.4 dated 2017-06-25

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Package photobiology updated to version 0.9.16 with previous version 0.9.15 dated 2017-04-29

Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima. Conversion between energy- and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision.
Author: Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiology versions 0.9.15 dated 2017-04-29 and 0.9.16 dated 2017-06-25

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Package opencpu updated to version 2.0.3 with previous version 2.0.2 dated 2017-06-17

Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between opencpu versions 2.0.2 dated 2017-06-17 and 2.0.3 dated 2017-06-25

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 30 files changed, 261 insertions(+), 138 deletions(-)

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Package net.security updated to version 0.3.0 with previous version 0.1.0 dated 2017-04-01

Title: Security Standards Data Sets
Description: Provides functions for security standards data management. It comes with data frames of 1000 observations for each security standard and updates are possible from official sources to build updated data sets.
Author: Humbert Costas [aut, cre], Arnau Sangra [ctb]
Maintainer: Humbert Costas <humbert.costas@gmail.com>

Diff between net.security versions 0.1.0 dated 2017-04-01 and 0.3.0 dated 2017-06-25

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New package leaflet.extras with initial version 0.2
Package: leaflet.extras
Type: Package
Title: Extra Functionality for 'leaflet' Package
Version: 0.2
Authors@R: c( person("Bhaskar", "Karambelkar", email = "bhaskarvk@gmail.com", role = c("aut", "cre")), person("Bangyou", "Zheng", email= "Bangyou.Zheng@csiro.au", role = c("ctb"), comment = "Leaflet-search and Leaflet-GPS plugin integration") )
Description: The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0), leaflet (>= 1.1.0)
Imports: shiny, htmlwidgets, htmltools, stringr, magrittr
Suggests: V8, dplyr, geojsonio, purrr, readr, rmapshaper, htmlTable, memoise
URL: https://github.com/bhaskarvk/leaflet.extras
BugReports: https://github.com/bhaskarvk/leaflet.extras/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-25 14:49:28 UTC; bhaskar
Author: Bhaskar Karambelkar [aut, cre], Bangyou Zheng [ctb] (Leaflet-search and Leaflet-GPS plugin integration)
Maintainer: Bhaskar Karambelkar <bhaskarvk@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-25 15:22:08 UTC

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New package leaflet.esri with initial version 0.2
Package: leaflet.esri
Type: Package
Title: 'ESRI' Bindings for the 'leaflet' Package
Version: 0.2
Authors@R: person("Bhaskar", "Karambelkar", email = "bhaskarvk@gmail.com", role = c("aut", "cre"))
Description: An add-on package to the 'leaflet' package, which provides bindings for 'ESRI' services. This package allows a user to add 'ESRI' provided services such as 'MapService', 'ImageMapService', 'TiledMapService' etc. to a 'leaflet' map.
License: GPL-3 | file LICENSE
Depends: R (>= 3.1.0), leaflet (>= 1.1.0), leaflet.extras (>= 0.2)
Encoding: UTF-8
LazyData: true
Imports: shiny, htmlwidgets, htmltools, magrittr
Suggests: V8, dplyr, geojsonio, purrr, readr, stringr, rmapshaper, htmlTable, memoise
URL: https://github.com/bhaskarvk/leaflet.esri
BugReports: https://github.com/bhaskarvk/leaflet.esri/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-25 15:50:01 UTC; bhaskar
Author: Bhaskar Karambelkar [aut, cre]
Maintainer: Bhaskar Karambelkar <bhaskarvk@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-25 16:06:42 UTC

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Package ggsignif updated to version 0.3.0 with previous version 0.2.0 dated 2017-04-26

Title: Significance Brackets for 'ggplot2'
Description: Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.
Author: Constantin Ahlmann-Eltze [aut, cre]
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>

Diff between ggsignif versions 0.2.0 dated 2017-04-26 and 0.3.0 dated 2017-06-25

 DESCRIPTION                                   |   14 +-
 MD5                                           |   34 ++++--
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Package endorse updated to version 1.6.0 with previous version 1.5.2 dated 2017-04-18

Title: Bayesian Measurement Models for Analyzing Endorsement Experiments
Description: Fit the hierarchical and non-hierarchical Bayesian measurement models proposed by Bullock, Imai, and Shapiro (2011) <DOI:10.1093/pan/mpr031> to analyze endorsement experiments. Endorsement experiments are a survey methodology for eliciting truthful responses to sensitive questions. This methodology is helpful when measuring support for socially sensitive political actors such as militant groups. The model is fitted with a Markov chain Monte Carlo algorithm and produces the output containing draws from the posterior distribution.
Author: Yuki Shiraito [aut, cre], Kosuke Imai [aut], Bryn Rosenfeld [ctb]
Maintainer: Yuki Shiraito <shiraito@princeton.edu>

Diff between endorse versions 1.5.2 dated 2017-04-18 and 1.6.0 dated 2017-06-25

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Package pcaPP updated to version 1.9-70 with previous version 1.9-61 dated 2016-10-10

Title: Robust PCA by Projection Pursuit
Description: Provides functions for robust PCA by projection pursuit.
Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

Diff between pcaPP versions 1.9-61 dated 2016-10-10 and 1.9-70 dated 2017-06-25

 ChangeLog       |   16 ++++++++++++----
 DESCRIPTION     |    8 ++++----
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New package factorMerger with initial version 0.3
Package: factorMerger
Title: Hierarchical Algorithm for Post-Hoc Testing
Version: 0.3
Authors@R: c( person("Agnieszka", "Sitko", email = "ag.agnieszka.sitko@gmail.com", role = c("aut", "cre")), person("Przemyslaw", "Biecek", email = "przemyslaw.biecek@gmail.com", role = c("aut","ths")) )
Description: A set of tools to support results of post-hoc testing and enable to extract hierarchical structure of factors. Work on this package was financially supported by the 'NCN Opus grant 2016/21/B/ST6/02176'.
Depends: R (>= 3.2.3)
License: GPL
Encoding: UTF-8
LazyData: true
Imports: ggplot2, dplyr, ggrepel, reshape2, colorRamps, Hotelling, vegan, proxy, MASS, survminer, gridExtra, scales, grid, mvtnorm, knitr, magrittr, survival, ggpubr, forcats, agricolae
RoxygenNote: 6.0.1
URL: https://github.com/geneticsMiNIng/factorMerger
Suggests: rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-06-25 11:23:56 UTC; agnieszka
Author: Agnieszka Sitko [aut, cre], Przemyslaw Biecek [aut, ths]
Maintainer: Agnieszka Sitko <ag.agnieszka.sitko@gmail.com>
Repository: CRAN
Date/Publication: 2017-06-25 12:22:29 UTC

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New package SeqKat with initial version 0.0.4
Package: SeqKat
Type: Package
Title: Detection of Kataegis
Version: 0.0.4
Date: 2017-06-16
Author: Fouad Yousif, Xihui Lin, Fan Fan, Christopher Lalansingh
Maintainer: Paul C. Boutros <Paul.Boutros@oicr.on.ca>
Description: Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. SeqKat reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Upon publication of the paper describing the methods used in this package, a reference will be added here.
Depends: R (>= 2.15.1), foreach, doParallel
Imports: Rcpp(>= 0.11.0)
LinkingTo: Rcpp
Suggests: testthat, doMC, rmarkdown, knitr
License: GPL-2
LazyLoad: yes
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-06-25 06:22:12 UTC; clalansingh
Repository: CRAN
Date/Publication: 2017-06-25 07:10:11 UTC

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New package RegularizedSCA with initial version 0.4.2
Package: RegularizedSCA
Type: Package
Title: Regularized Simultaneous Component Based Data Integration
Version: 0.4.2
Authors@R: c(person(given = "Zhengguo", family = "Gu", role = c("aut", "cre"), email = "z.gu@uvt.nl"), person(given = "Katrijn", family = "Van Deun", role = "aut"))
Description: It performs regularized simultaneous component based data integration for multiblock data.
Depends: R (>= 2.10)
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown
Imports: gtools, psych, RGCCA, ggplot2, stats, utils, graphics
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-06-24 11:51:40 UTC; Zhengguo
Author: Zhengguo Gu [aut, cre], Katrijn Van Deun [aut]
Maintainer: Zhengguo Gu <z.gu@uvt.nl>
Repository: CRAN
Date/Publication: 2017-06-25 07:14:44 UTC

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New package ratios with initial version 1.0.0
Package: ratios
Type: Package
Title: Ratios Between Two Data Sets and Correction for Adhering Particles on Plants
Version: 1.0.0
Author: Solveig Pospiech [aut, cre], Wiebke Fahlbusch [ctb]
Maintainer: Solveig Pospiech <s.pospiech@gmx.de>
Description: Calculation of ratios between two data sets containing environmental data like element concentrations by different methods. Additionally plant element concentrations can be corrected for adhering particles (soil, airborne dust).
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R (>= 2.10)
Imports: stringr, data.table
NeedsCompilation: no
Packaged: 2017-06-24 18:14:25 UTC; solveig
Repository: CRAN
Date/Publication: 2017-06-25 07:13:54 UTC

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New package later with initial version 0.3
Package: later
Type: Package
Title: Utilities for Delaying Function Execution
Version: 0.3
Authors@R: c( person("Joe", "Cheng", role = c("aut", "cre"), email = "joe@rstudio.com"), person(family = "RStudio", role = "cph"), person("Marcus", "Geelnard", role = c("ctb", "cph"), comment = "TinyThread library, http://tinythreadpp.bitsnbites.eu/") )
Description: Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied.
URL: https://github.com/r-lib/later
BugReports: https://github.com/r-lib/later/issues
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.9), rlang
LinkingTo: Rcpp, BH
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-06-24 07:40:04 UTC; jcheng
Author: Joe Cheng [aut, cre], RStudio [cph], Marcus Geelnard [ctb, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)
Maintainer: Joe Cheng <joe@rstudio.com>
Repository: CRAN
Date/Publication: 2017-06-25 07:15:14 UTC

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Package googleway updated to version 2.2.0 with previous version 2.0.0 dated 2017-05-01

Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a Google Map from R and overlay it with shapes and markers. Also provides access to Google Maps APIs, including places, directions, roads, distances, geocoding, elevation and timezone.
Author: David Cooley [aut, cre], Paulo Barcelos [ctb] (Author of c++ decode_pl), Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between googleway versions 2.0.0 dated 2017-05-01 and 2.2.0 dated 2017-06-25

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 googleway-2.2.0/googleway/NAMESPACE                               |    4 
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Package FuzzyLP updated to version 0.1-4 with previous version 0.1-3 dated 2015-07-08

Title: Fuzzy Linear Programming
Description: Provides methods to solve Fuzzy Linear Programming Problems with fuzzy constraints (following different approaches proposed by Verdegay, Zimmermann, Werners and Tanaka), fuzzy costs, and fuzzy technological matrix.
Author: Carlos A. Rabelo [aut, cre], Pablo J. Villacorta [ctb]
Maintainer: Carlos A. Rabelo <carabelo@gmail.com>

Diff between FuzzyLP versions 0.1-3 dated 2015-07-08 and 0.1-4 dated 2017-06-25

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 FuzzyLP-0.1-4/FuzzyLP/R/CosFuz.R                |  831 ++++++++++++------------
 FuzzyLP-0.1-4/FuzzyLP/R/GenFuz.R                |  296 ++++----
 FuzzyLP-0.1-4/FuzzyLP/man/FCLP.Beta.Rd          |  163 ++--
 FuzzyLP-0.1-4/FuzzyLP/man/FCLP.Obj.Rd           |  257 +++----
 FuzzyLP-0.1-4/FuzzyLP/man/FOLP_Ordering.Rd      |  179 ++---
 FuzzyLP-0.1-4/FuzzyLP/man/FOLP_Posib.Rd         |  122 +--
 FuzzyLP-0.1-4/FuzzyLP/man/FOLP_Repres.Rd        |  230 +++---
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 FuzzyLP-0.1-4/FuzzyLP/man/crispLP.Rd            |   89 +-
 16 files changed, 1248 insertions(+), 1230 deletions(-)

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Package CDM updated to version 5.7-16 with previous version 5.6-16 dated 2017-06-17

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous data. This package enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the multidimensional linear compensatory item response model and the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between CDM versions 5.6-16 dated 2017-06-17 and 5.7-16 dated 2017-06-25

 DESCRIPTION                         |    9 +--
 MD5                                 |   28 ++++++---
 NAMESPACE                           |    8 ++
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 19 files changed, 119 insertions(+), 107 deletions(-)

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Permanent link

New package bssm with initial version 0.1.0
Package: bssm
Type: Package
Title: Bayesian Inference of State Space Models
Version: 0.1.0
Date: 2017-06-24
Author: Jouni Helske, Matti Vihola
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo and importance sampling type corrected Markov chain Monte Carlo. Gaussian, Poisson, binomial, or negative binomial observation densities and Gaussian state dynamics, as well as general non-linear Gaussian models are supported.
License: GPL (>= 2)
Depends: R (>= 3.1.3)
Suggests: KFAS (>= 1.2.1), knitr (>= 1.11), rmarkdown (>= 0.8.1), testthat, bayesplot
Imports: coda (>= 0.18-1), diagis, ggplot2 (>= 2.0.0), Rcpp (>= 0.12.3)
LinkingTo: BH, Rcpp, RcppArmadillo, ramcmc
SystemRequirements: C++11
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-06-24 13:53:46 UTC; jouni
Repository: CRAN
Date/Publication: 2017-06-25 07:14:15 UTC

More information about bssm at CRAN
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Package bazar updated to version 0.1.6 with previous version 0.1.4 dated 2017-01-14

Title: Miscellaneous Basic Functions
Description: A collection of miscellaneous functions for copying objects to the clipboard ('Copy'); manipulating strings ('concat', 'mgsub', 'trim', 'verlan'); loading or showing packages ('library_with_dep', 'require_with_dep', 'sessionPackages'); creating or testing for named lists ('nlist', 'as.nlist', 'is.nlist'), formulas ('is.formula'), empty objects ('as.empty', 'is.empty'), whole numbers ('as.wholenumber', 'is.wholenumber'); testing for equality ('almost.equal', 'almost.zero'); getting modified versions of usual functions ('rle2', 'sumNA'); making a pause or a stop ('pause', 'stopif'); and others ('erase', '%nin%', 'unwhich').
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>

Diff between bazar versions 0.1.4 dated 2017-01-14 and 0.1.6 dated 2017-06-25

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 29 files changed, 63 insertions(+), 71 deletions(-)

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Package bayesm updated to version 3.1-0 with previous version 3.0-2 dated 2015-06-20

Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda, Rossi 2009) For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>

Diff between bayesm versions 3.0-2 dated 2015-06-20 and 3.1-0 dated 2017-06-25

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Sat, 24 Jun 2017

Package R2MLwiN updated to version 0.8-4 with previous version 0.8-3 dated 2016-09-07

Title: Running 'MLwiN' from Within R
Description: An R command interface to the 'MLwiN' multilevel modelling software package.
Author: Zhengzheng Zhang [aut, cre], Chris Charlton [aut], Richard Parker [aut], George Leckie [aut], William Browne [aut]
Maintainer: Zhengzheng Zhang <zhengzheng236@gmail.com>

Diff between R2MLwiN versions 0.8-3 dated 2016-09-07 and 0.8-4 dated 2017-06-24

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Package ggiraph updated to version 0.4.0 with previous version 0.3.3 dated 2017-03-24

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

Diff between ggiraph versions 0.3.3 dated 2017-03-24 and 0.4.0 dated 2017-06-24

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Package ggExtra updated to version 0.7 with previous version 0.6 dated 2016-11-11

Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main function is ggMarginal(), which can be used to add marginal histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre], Christopher Baker [ctb]
Maintainer: Dean Attali <daattali@gmail.com>

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Package aSPU updated to version 1.48 with previous version 1.47 dated 2017-05-21

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single nucleotide polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended 'Simes' procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

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Package sys updated to version 1.4 with previous version 1.3 dated 2017-04-20

Title: Portable System Utilities
Description: Powerful replacements for base system2 with consistent behavior across platforms. Supports interruption, background tasks, and full control over 'STDOUT' / 'STDERR' binary or text streams. On Unix systems the package also has 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], Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package stacomirtools updated to version 0.5.2 with previous version 0.5.0 dated 2016-08-20

Title: 'ODBC' Connection Class for Package stacomiR
Description: S4 class wrappers for the 'ODBC' connection, also provides some utilities to paste small datasets to clipboard, rename columns. It is used by the package 'stacomiR' for connections to the database. Development versions of 'stacomiR' are available in R-forge.
Author: Cedric Briand [aut, cre]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>

Diff between stacomirtools versions 0.5.0 dated 2016-08-20 and 0.5.2 dated 2017-06-24

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Package spind updated to version 2.1.0 with previous version 2.0.1 dated 2017-04-07

Title: Spatial Methods and Indices
Description: Functions for spatial methods based on generalized estimating equations (GEE) and wavelet-revised methods (WRM), functions for scaling by wavelet multiresolution regression (WMRR), conducting multi-model inference, and stepwise model selection. Further, contains functions for spatially corrected model accuracy measures.
Author: Gudrun Carl [cre, aut], Ingolf Kuehn [aut], Sam Levin [aut]
Maintainer: Sam Levin <levisc8@gmail.com>

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Package PRIMsrc updated to version 0.7.1 with previous version 0.7.0 dated 2017-05-29

Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>

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Package MultiSkew updated to version 1.1.1 with previous version 1.1 dated 2017-06-14

Title: Measures, Tests and Removes Multivariate Skewness
Description: Computes the third multivariate cumulant of either the raw, centered or standardized data. Computes the main measures of multivariate skewness, together with their bootstrap distributions. Finally, computes the least skewed linear projections of the data.
Author: Cinzia Franceschini, Nicola Loperfido
Maintainer: Cinzia Franceschini <cinziafranceschini@msn.com>

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Package micompr updated to version 1.0.2 with previous version 1.0.1 dated 2016-08-04

Title: Multivariate Independent Comparison of Observations
Description: A procedure for comparing multivariate samples associated with different groups. It uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. The procedure is independent of the distributional properties of samples and automatically selects features that best explain their differences, avoiding manual selection of specific points or summary statistics. It is appropriate for comparing samples of time series, images, spectrometric measures or similar multivariate observations.
Author: Nuno Fachada [aut, cre]
Maintainer: Nuno Fachada <faken@fakenmc.com>

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 vignettes/paper.Rnw                  |  258 +++++++++++++++++++++++------------
 53 files changed, 452 insertions(+), 296 deletions(-)

More information about micompr at CRAN
Permanent link

Package generalhoslem updated to version 1.2.5 with previous version 1.2.4 dated 2016-12-16

Title: Goodness of Fit Tests for Logistic Regression Models
Description: Functions to assess the goodness of fit of binary, multinomial and ordinal logistic models. Included are the Hosmer-Lemeshow tests (binary, multinomial and ordinal) and the Lipsitz and Pulkstenis-Robinson tests (ordinal).
Author: Matthew Jay [aut, cre]
Maintainer: Matthew Jay <matthew.jay.15@ucl.ac.uk>

Diff between generalhoslem versions 1.2.4 dated 2016-12-16 and 1.2.5 dated 2017-06-24

 DESCRIPTION          |    8 ++++----
 MD5                  |   16 ++++++++--------
 R/lipsitz.test.R     |    2 +-
 R/logitgof.R         |    2 ++
 R/pulkrob.chisq.R    |    2 +-
 build/partial.rdb    |binary
 man/lipsitz.test.Rd  |    6 +++---
 man/logitgof.Rd      |    4 +++-
 man/pulkrob.chisq.Rd |    4 ++--
 9 files changed, 24 insertions(+), 20 deletions(-)

More information about generalhoslem at CRAN
Permanent link

Package RPostgreSQL updated to version 0.6-2 with previous version 0.4-1 dated 2016-05-08

Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. In order to build and install this package from source, 'PostgreSQL' itself must be present your system to provide 'PostgreSQL' functionality via its libraries and header files. These files are provided as 'postgresql-devel' package under some Linux distributions. On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga (during 2008), Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>

Diff between RPostgreSQL versions 0.4-1 dated 2016-05-08 and 0.6-2 dated 2017-06-24

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 RPostgreSQL-0.6-2/RPostgreSQL/NAMESPACE                                |    6 
 RPostgreSQL-0.6-2/RPostgreSQL/R/PostgreSQL.R                           |   34 
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 RPostgreSQL-0.6-2/RPostgreSQL/configure                                | 1892 ++++------
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Package evaluate updated to version 0.10.1 with previous version 0.10 dated 2016-10-11

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [cre, ctb], Michael Lawrence [ctb], Thomas Kluyver [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between evaluate versions 0.10 dated 2016-10-11 and 0.10.1 dated 2017-06-24

 DESCRIPTION               |   10 +++++-----
 MD5                       |   32 ++++++++++++++++----------------
 NAMESPACE                 |    3 +++
 NEWS                      |    6 ++++++
 R/parse.r                 |   10 ++++++++++
 man/create_traceback.Rd   |    1 +
 man/evaluate.Rd           |    1 +
 man/flush_console.Rd      |    1 +
 man/inject_funs.Rd        |    1 +
 man/is.message.Rd         |   12 +++++++++---
 man/line_prompt.Rd        |    1 +
 man/new_output_handler.Rd |    1 +
 man/parse_all.Rd          |    1 +
 man/replay.Rd             |    1 +
 man/set_hooks.Rd          |    1 +
 man/try_capture_stack.Rd  |    1 +
 man/watchout.Rd           |    1 +
 17 files changed, 60 insertions(+), 24 deletions(-)

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New package aphid with initial version 1.0.0
Package: aphid
Type: Package
Title: Analysis with Profile Hidden Markov Models
Version: 1.0.0
Authors@R: person("Shaun", "Wilkinson", email = "shaunpwilkinson@gmail.com", role = c("aut", "cre"))
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
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.
License: GPL-3
URL: http://github.com/shaunpwilkinson/aphid
BugReports: http://github.com/shaunpwilkinson/aphid/issues
LazyData: TRUE
SystemRequirements: GNU make
Depends: R(>= 3.0.0)
Imports: graphics, openssl, phylogram (>= 1.0.0), Rcpp (>= 0.12.5), stats
Suggests: ape (>= 3.0), knitr, rmarkdown, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-06-24 06:12:58 UTC; shaun
Repository: CRAN
Date/Publication: 2017-06-24 07:22:46 UTC

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New package windfarmGA with initial version 1.0
Package: windfarmGA
Type: Package
Title: Genetic Algorithm for Wind Farm Layout Optimization
Version: 1.0
Date: 2017-06-20
Author: Sebastian Gatscha
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Description: The genetic algorithm is designed to optimize small wind farms up to 50 turbines. The algorithm works with a fixed amount of turbines, a fixed rotor radius and a mean wind speed value for every incoming wind direction. If required it can include a terrain effect model, which downloads an 'SRTM' elevation model automatically and loads a Corine Land Cover raster, which has to be downloaded previously. Further information can be found at the description of the function 'windfarmGA'. To start an optimization run, either the function 'windfarmGA' or 'genAlgo' can be used. The function 'windfarmGA' checks the user inputs interactively and then runs the function 'genAlgo'. If the input parameters are already known, an optimization can be run directly via the function 'genAlgo'. Their output is identical.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.2.3)
Imports: rgdal (>= 1.0-4), raster (>= 2.5-2), sp (>= 1.2-2), dplyr (>= 0.5.0), data.table (>= 1.9.6), gtools (>= 3.5.0), maptools (>= 0.8-36), calibrate (>= 1.7.2), geoR (>= 1.7-5.1), gstat (>= 1.0-26), ggplot2 (>= 2.2.0), RColorBrewer (>= 1.1-2), rgeos (>= 0.3-11), RgoogleMaps (>= 1.2.0.7), googleVis (>= 0.5.9), rgl (>= 0.96.0), grDevices, graphics, stats, utils
Suggests: magrittr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-23 20:08:54 UTC; Bobo
Repository: CRAN
Date/Publication: 2017-06-24 05:54:16 UTC

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New package DZEXPM with initial version 1.0
Package: DZEXPM
Type: Package
Title: Estimation and Prediction of Skewed Spatial Processes
Version: 1.0
Date: 2017-06-24
Author: Jiangyan Wang, Miao Yang and Anandamayee Majumdar
Maintainer: "Jiangyan Wang" <jiangyanwang@nau.edu.cn>
Description: A collection of functions designed to estimate and predict skewed spatial processes, and a real data set.
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2017-06-24 04:41:05 UTC; Jiangyan
Repository: CRAN
Date/Publication: 2017-06-24 05:49:25 UTC

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Package ddpcr updated to version 1.8 with previous version 1.6 dated 2016-11-11

Title: Analysis and Visualization of Droplet Digital PCR in R and on the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between ddpcr versions 1.6 dated 2016-11-11 and 1.8 dated 2017-06-24

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New package nlsrk with initial version 1.1
Package: nlsrk
Version: 1.1
Date: 2017-06-22
Title: Runge-Kutta Solver for Function nls()
Author: Jean-Sebastien Pierre <jean-sebastien.pierre@univ-rennes1.fr>
Maintainer: Jean-Sebastien Pierre <jean-sebastien.pierre@univ-rennes1.fr>
Depends: R (>= 3.0.0)
Description: Performs univariate or multivariate computation of a single ODE or of a set of ODE (ordinary differential equations).
License: GPL (>= 2)
URL: none
NeedsCompilation: no
Packaged: 2017-06-23 20:53:09 UTC; jpierre
Repository: CRAN
Date/Publication: 2017-06-23 23:01:24 UTC

More information about nlsrk at CRAN
Permanent link

Fri, 23 Jun 2017

Package visreg updated to version 2.4-1 with previous version 2.4-0 dated 2017-06-09

Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'lmer', 'randomForest', etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

Diff between visreg versions 2.4-0 dated 2017-06-09 and 2.4-1 dated 2017-06-23

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Package rLakeAnalyzer updated to version 1.8.7 with previous version 1.8.3 dated 2016-05-20

Title: Lake Physics Tools
Description: Standardized methods for calculating common important derived physical features of lakes including water density based based on temperature, thermal layers, thermocline depth, lake number, Wedderburn number, Schmidt stability and others.
Author: Luke Winslow, Jordan Read, Richard Woolway, Jennifer Brentrup, Taylor Leach, Jake Zwart
Maintainer: Luke Winslow <lawinslow@gmail.com>

Diff between rLakeAnalyzer versions 1.8.3 dated 2016-05-20 and 1.8.7 dated 2017-06-23

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Package rcompanion updated to version 1.5.7 with previous version 1.5.6 dated 2017-04-21

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of Extension Education Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

Diff between rcompanion versions 1.5.6 dated 2017-04-21 and 1.5.7 dated 2017-06-23

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Package liureg updated to version 1.01 with previous version 1.0 dated 2017-03-08

Title: Liu Regression with Liu Biasing Parameters and Statistics
Description: Linear Liu regression coefficient's estimation and testing with different Liu related measures such as MSE, R-squared etc.
Author: Muhammad Imdadullah, Dr. Muhammad Aslam
Maintainer: Muhammad Imdadullah <mimdadasad@gmail.com>

Diff between liureg versions 1.0 dated 2017-03-08 and 1.01 dated 2017-06-23

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Package WRTDStidal updated to version 1.1.0 with previous version 1.0.1 dated 2016-11-07

Title: Weighted Regression for Water Quality Evaluation in Tidal Waters
Description: An adaptation for estuaries (tidal waters) of weighted regression on time, discharge, and season to evaluate trends in water quality time series.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>

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Package webutils updated to version 0.6 with previous version 0.5 dated 2017-04-28

Title: Utility Functions for Developing Web Applications
Description: High performance in-memory http request parser for application/json, multipart/form-data, and application/x-www-form-urlencoded. Includes live demo of hosting and parsing multipart forms with either 'httpuv' or 'Rhttpd'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between webutils versions 0.5 dated 2017-04-28 and 0.6 dated 2017-06-23

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Package sf updated to version 0.5-1 with previous version 0.5-0 dated 2017-06-15

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to Proj.4 for projection conversions and datum transformations.
Author: Edzer Pebesma [aut, cre], Roger Bivand [ctb], Ian Cook [ctb], Tim Keitt [ctb], Michael Sumner [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb], Etienne Racine [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package rvg updated to version 0.1.4 with previous version 0.1.3 dated 2017-03-12

Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for 'SVG', 'DrawingML' for Microsoft Word, PowerPoint and Excel. Functions extending package 'officer' are provided to embed 'DrawingML' graphics into 'Microsoft PowerPoint' documents.
Author: David Gohel [aut, cre], Bob Rudis [ctb] (the javascript code used by function set_attr), Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package RSocrata updated to version 1.7.3-2 with previous version 1.7.2-12 dated 2017-04-19

Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with Socrata open data portals <http://dev.socrata.com>. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to Socrata portals directly from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., and John Malc
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>

Diff between RSocrata versions 1.7.2-12 dated 2017-04-19 and 1.7.3-2 dated 2017-06-23

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Package precrec updated to version 0.8.0 with previous version 0.7.1 dated 2017-04-07

Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between precrec versions 0.7.1 dated 2017-04-07 and 0.8.0 dated 2017-06-23

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 precrec-0.8.0/precrec/tests/testthat/test_g_datamatrix1_curves.R     |   95 ++++
 precrec-0.8.0/precrec/tests/testthat/test_g_datamatrix2_points.R     |   96 ++++
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New package IceCast with initial version 1.1.0
Package: IceCast
Type: Package
Title: Apply Statistical Post-Processing to Improve Sea Ice Predictions
Version: 1.1.0
Author: Hannah M. Director, Adrian E. Raftery, and Cecilia M. Bitz
Maintainer: Hannah M. Director <direch@uw.edu>
Description: Tools for modeling and correcting biases in sea ice predictions obtained from dynamical models.
License: GPL (>= 2)
Depends: R (>= 2.10), rgeos, sp
Imports: ncdf4, maptools, MASS, raster, methods, utils
Suggests: geosphere, fields, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-23 17:19:08 UTC; hdirector
Repository: CRAN
Date/Publication: 2017-06-23 19:03:58 UTC

More information about IceCast at CRAN
Permanent link

Package BioInstaller updated to version 0.1.2 with previous version 0.1.1 dated 2017-05-25

Title: Lightweight Biology Software Installer
Description: Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

Diff between BioInstaller versions 0.1.1 dated 2017-05-25 and 0.1.2 dated 2017-06-23

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New package Rcriticor with initial version 1.1
Package: Rcriticor
Version: 1.1
Type: Package
Title: Critical Periods
Date: 2017-06-18
Author: Jean-Sebastien PIERRE [aut,cre]
Maintainer: Jean-Sebastien Pierre <jean-sebastien.pierre@univ-rennes1.fr>
Depends: R (>= 3.2.0)
Description: Pierre's correlogram. Research of critical periods in the past. Integrates a time series in a given window.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2017-06-23 15:07:57 UTC; jpierre
Repository: CRAN
Date/Publication: 2017-06-23 16:05:37 UTC

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New package cbar with initial version 0.1.0
Package: cbar
Type: Package
Title: Contextual Bayesian Anomaly Detection in R
Version: 0.1.0
Date: 2017-06-22
Description: Detect contextual anomalies in time-series data with Bayesian data analysis. It focuses on determining a normal range of target value, and provides simple-to-use functions to abstract the outcome.
Author: Kim Seonghyun [aut, cre]
Maintainer: Kim Seonghyun <shyeon.kim@scipi.net>
Depends: R (>= 3.3.0)
Imports: Boom, bsts, dplyr, magrittr, ggplot2, stats
Suggests: datasets, knitr, testthat
License: Apache License 2.0 | file LICENSE
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 6.0.1
BugReports: https://github.com/zedoul/cbar/issues
NeedsCompilation: no
Packaged: 2017-06-23 14:30:11 UTC; zedoul
Repository: CRAN
Date/Publication: 2017-06-23 16:05:39 UTC

More information about cbar at CRAN
Permanent link

Package dartR updated to version 0.80 with previous version 0.79 dated 2017-06-23

Title: Importing and Analysing Snp and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis
Description: Functions are provided that facilitate the import and analysis of snp and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of snp and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE. Other functions are available for visualization after PCoA, or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip packages etc.
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>

Diff between dartR versions 0.79 dated 2017-06-23 and 0.80 dated 2017-06-23

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 vignettes/IntroTutorial_dartR.Rmd |   16 ++--
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More information about dartR at CRAN
Permanent link

Package bigrquery updated to version 0.4.0 with previous version 0.3.0 dated 2016-06-28

Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between bigrquery versions 0.3.0 dated 2016-06-28 and 0.4.0 dated 2017-06-23

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Package bmlm updated to version 1.3.0 with previous version 1.2.10 dated 2017-02-17

Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre]
Maintainer: Matti Vuorre <mv2521@columbia.edu>

Diff between bmlm versions 1.2.10 dated 2017-02-17 and 1.3.0 dated 2017-06-23

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Package spsann updated to version 2.1-0 with previous version 2.0-0 dated 2016-03-15

Title: Optimization of Sample Configurations using Spatial Simulated Annealing
Description: Methods to optimize sample configurations using spatial simulated annealing. Multiple objective functions are implemented for various purposes, such as variogram estimation, spatial trend estimation and spatial interpolation. A general purpose spatial simulated annealing function enables the user to define his/her own objective function. Solutions for augmenting existing sample configurations and solving multi-objective optimization problems are available as well.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths], Gustavo de Mattos Vasques [ths], Gerard B M Heuvelink [ths], Edzer Pebesma [ctb], Jon Skoien [ctb], Joshua French [ctb], Pierre Roudier [ctb], Dick Brus [ctb], Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

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More information about spsann at CRAN
Permanent link

Package spmoran updated to version 0.1.1 with previous version 0.1.0 dated 2017-03-12

Title: Moran's Eigenvector-Based Spatial Regression Models
Description: Functions for estimating fixed and random effects eigenvector spatial filtering models.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <murakami_daisuke_t@yahoo.co.jp>

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Package reticulate updated to version 0.9 with previous version 0.8 dated 2017-05-22

Title: R Interface to Python
Description: R interface to Python modules, classes, and functions. When calling into Python R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types. Compatible with all versions of Python >= 2.7.
Author: JJ Allaire [aut, cre], Kevin Ushey [ctb], RStudio [cph, fnd], Yuan Tang [aut, cph], Dirk Eddelbuettel [ctb, cph], Bryan Lewis [ctb, cph], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between reticulate versions 0.8 dated 2017-05-22 and 0.9 dated 2017-06-23

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Package memapp updated to version 2.2 with previous version 2.1 dated 2017-06-08

Title: The Moving Epidemic Method Web Application
Description: Web application created in the Shiny framework for the 'mem' R package.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>

Diff between memapp versions 2.1 dated 2017-06-08 and 2.2 dated 2017-06-23

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Package mem updated to version 2.8 with previous version 2.7 dated 2017-06-08

Title: The Moving Epidemic Method R Package
Description: Tools to model influenza epidemics and to monitor influenza surveillance.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>

Diff between mem versions 2.7 dated 2017-06-08 and 2.8 dated 2017-06-23

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Package fsia updated to version 1.1.1 with previous version 1.1 dated 2016-12-07

Title: Import and Analysis of OMR Data from FormScanner
Description: Import data of tests and questionnaires from FormScanner. FormScanner is an open source software that converts scanned images to data using optical mark recognition (OMR) and it can be downloaded from <http://sourceforge.net/projects/formscanner/>. The spreadsheet file created by FormScanner is imported in a convenient format to perform the analyses provided by the package. These analyses include the conversion of multiple responses to binary (correct/incorrect) data, the computation of the number of corrected responses for each subject or item, scoring using weights,the computation and the graphical representation of the frequencies of the responses to each item and the report of the responses of a few subjects.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>

Diff between fsia versions 1.1 dated 2016-12-07 and 1.1.1 dated 2017-06-23

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New package nsROC with initial version 1.0
Package: nsROC
Type: Package
Title: Non-Standard ROC Curve Analysis
Version: 1.0
Author: Sonia Perez Fernandez
Maintainer: Sonia Perez Fernandez <uo217889@uniovi.es>
Description: Tools for estimating Receiver Operating Characteristic (ROC) curves, building confidence bands, comparing several curves both for dependent and independent data, estimating the cumulative-dynamic ROC curve in presence of censored data, and performing meta-analysis studies, among others.
License: GPL (>= 3)
Depends: R (>= 2.10)
LazyData: TRUE
Imports: stats, methods, utils, graphics, sde, survival
Suggests: mvtnorm
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-06-23 10:54:31 UTC; user2
Repository: CRAN
Date/Publication: 2017-06-23 12:36:14 UTC

More information about nsROC at CRAN
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Package rem updated to version 1.2.8 with previous version 1.1.2 dated 2016-02-19

Title: Relational Event Models (REM)
Description: Calculate endogenous network effects in event sequences and fit relational event models (REM): Using network event sequences (where each tie between a sender and a target in a network is time-stamped), REMs can measure how networks form and evolve over time. Endogenous patterns such as popularity effects, inertia, similarities, cycles or triads can be calculated and analyzed over time.
Author: Laurence Brandenberger
Maintainer: Laurence Brandenberger <laurence.brandenberger@eawag.ch>

Diff between rem versions 1.1.2 dated 2016-02-19 and 1.2.8 dated 2017-06-23

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Package nmaINLA updated to version 0.1.1 with previous version 0.1.0 dated 2017-06-20

Title: Network Meta-Analysis using Integrated Nested Laplace Approximations
Description: Performs network meta-analysis using integrated nested Laplace approximations ('INLA'). Includes methods to assess the heterogeneity and inconsistency in the network. Contains more than ten different network meta-analysis data. 'INLA' package can be obtained from <http://www.r-inla.org>. We recommend the testing version.
Author: Burak Kuersad Guenhan [aut, cre]
Maintainer: Burak Kuersad Guenhan <burak.gunhan@med.uni-goettingen.de>

Diff between nmaINLA versions 0.1.0 dated 2017-06-20 and 0.1.1 dated 2017-06-23

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Package mljar updated to version 0.1.1 with previous version 0.1.0 dated 2017-06-01

Title: R API for MLJAR
Description: Provides an R API wrapper for 'mljar.com', a web service allowing for on-line training for machine learning models (see <https://mljar.com> for more information).
Author: Dominik Krzemiński <raymon92@gmail.com>
Maintainer: Piotr Płoński <contact@mljar.com>

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Package h2o updated to version 3.10.5.2 with previous version 3.10.4.6 dated 2017-05-02

Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source math engine for big data that computes parallel distributed machine learning algorithms such as generalized linear models, gradient boosting machines, random forests, and neural networks (deep learning) within various cluster environments.
Author: The H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>

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New package tbl2xts with initial version 0.1.0
Package: tbl2xts
Version: 0.1.0
Date: 2017-06-20
Type: Package
Title: Convert Tibbles or Data Frames to Xts Easily
Author: Nico Katzke
Description: Facilitate the movement between data frames to 'xts'. Particularly useful when moving from 'tidyverse' to the widely used 'xts' package, which is the input format of choice to various other packages. It also allows the user to use a 'spread_by' argument for a character column 'xts' conversion.
Maintainer: Nico Katzke <nfkatzke@gmail.com>
Depends: R (>= 3.2.1)
Imports: xts, zoo, dplyr, lazyeval, PerformanceAnalytics
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.0
Suggests: knitr, rmarkdown
Repository: CRAN
NeedsCompilation: yes
ByteCompile: yes
VignetteBuilder: knitr
Packaged: 2017-06-23 08:54:22 UTC; nicokatzke
Date/Publication: 2017-06-23 09:13:13 UTC

More information about tbl2xts at CRAN
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Package odbc updated to version 1.1.0 with previous version 1.0.1 dated 2017-02-07

Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut, cre], Hadley Wickham [aut], lexicalunit [cph] (nanodbc library), Google Inc. [cph] (cctz library), RStudio [cph, fnd]
Maintainer: Jim Hester <james.hester@rstudio.com>

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More information about odbc at CRAN
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Package imputeTestbench updated to version 3.0.1 with previous version 3.0.0 dated 2016-11-03

Title: Test Bench for the Comparison of Imputation Methods
Description: Provides a test bench for the comparison of missing data imputation methods in uni-variate time series. Imputation methods are compared using different error metrics. Proposed imputation methods and alternative error metrics can be used.
Author: Neeraj Bokde [aut], Marcus W. Beck [cre, aut]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>

Diff between imputeTestbench versions 3.0.0 dated 2016-11-03 and 3.0.1 dated 2017-06-23

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Package corset updated to version 0.1-4 with previous version 0.1-3 dated 2017-03-29

Title: Arbitrary Bounding of Series and Time Series Objects
Description: Set of methods to constrain numerical series and time series within arbitrary boundaries.
Author: Fran Urbano
Maintainer: Fran Urbano <viraltux@gmail.com>

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Package vdmR updated to version 0.2.4 with previous version 0.2.3 dated 2016-12-05

Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding interactive functions to 'ggplot2' graphics. Brushing and linking between the multiple plots is one of the main feature of this package. Currently scatter plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>

Diff between vdmR versions 0.2.3 dated 2016-12-05 and 0.2.4 dated 2017-06-23

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Package surv2sampleComp updated to version 1.0-5 with previous version 1.0-4 dated 2014-07-10

Title: Inference for Model-Free Between-Group Parameters for Censored Survival Data
Description: Performs inference of several model-free group contrast measures, which include difference/ratio of cumulative incidence rates at given time points, quantiles, and restricted mean survival times (RMST). Two kinds of covariate adjustment procedures (i.e., regression and augmentation) for inference of the metrics based on RMST are also included.
Author: Lu Tian, Hajime Uno, Miki Horiguchi
Maintainer: Miki Horiguchi <horiguchimiki@gmail.com>

Diff between surv2sampleComp versions 1.0-4 dated 2014-07-10 and 1.0-5 dated 2017-06-23

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 17 files changed, 200 insertions(+), 204 deletions(-)

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New package SCAT with initial version 0.3.0
Package: SCAT
Type: Package
Title: Summary based Conditional Association Test
Version: 0.3.0
Date: 2017-06-22
Author: Han Zhang, Kai Yu
Maintainer: Han Zhang <han.zhang2@nih.gov>
Depends: stats, utils
Description: Conditional association test based on summary data from genome-wide association study (GWAS) adjusting for heterogeneity in SNP coverage.
License: GPL-2 | GPL-3
LazyData: TRUE
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2017-06-23 03:47:07 UTC; zhangh12
Repository: CRAN
Date/Publication: 2017-06-23 06:37:18 UTC

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New package origami with initial version 0.8.0
Package: origami
Title: Generalized Framework for Cross-Validation
Version: 0.8.0
Authors@R: c( person("Jeremy", "Coyle", email = "jeremyrcoyle@gmail.com", role = c("aut", "cre", "cph")), person("Nima", "Hejazi", email = "nh@nimahejazi.org", role = "ctb"))
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>
Description: Provides a general framework for the application of cross-validation schemes to particular functions. By allowing arbitrary lists of results, origami accommodates a range of cross-validation applications.
Depends: R (>= 3.0.0),
Imports: abind, methods, data.table, future, listenv
Suggests: future.batchtools, testthat, class, rmarkdown, knitr, forecast, randomForest
License: GPL-3
URL: https://github.com/jeremyrcoyle/origami
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-22 22:25:09 UTC; jrcoyle
Author: Jeremy Coyle [aut, cre, cph], Nima Hejazi [ctb]
Repository: CRAN
Date/Publication: 2017-06-23 06:40:44 UTC

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New package m2r with initial version 1.0.0
Package: m2r
Type: Package
Title: Macaulay2 in R
Version: 1.0.0
Authors@R: c(person("David", "Kahle", email = "david.kahle@gmail.com", role = c("aut", "cph", "cre")), person("Christopher", "O'Neill", email = "musicman3320@gmail.com", role = c("aut", "cph")), person("Jeff", "Sommars", email = "sommars1@uic.edu", role = c("aut", "cph")))
Maintainer: David Kahle <david.kahle@gmail.com>
Description: Persistent interface to Macaulay2 (<http://www.math.uiuc.edu/Macaulay2/>) and front-end tools facilitating its use in the R ecosystem.
License: GPL-2
LazyData: TRUE
Depends: mpoly (>= 1.0.5)
Imports: stringr, memoise, pryr, gmp
SystemRequirements: Macaulay2 <http://www.math.uiuc.edu/Macaulay2/>
Suggests: knitr, rmarkdown, testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-22 19:46:35 UTC; david_kahle
Author: David Kahle [aut, cph, cre], Christopher O'Neill [aut, cph], Jeff Sommars [aut, cph]
Repository: CRAN
Date/Publication: 2017-06-23 06:40:14 UTC

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Package JumpTest updated to version 0.0.1 with previous version 0.0.0.9 dated 2017-06-22

Title: Financial Jump Detection
Description: A fast simulation on stochastic volatility model, with jump tests, p-values pooling, and FDR adjustments.
Author: Kaiqiao Li [aut, cre], Pei Fen Kuan [aut], Kan He [ctb], Lizhou Nie [ctb], Wei Zhu [ctb]
Maintainer: Kaiqiao Li <kaiqiao.li@stonybrook.edu>

Diff between JumpTest versions 0.0.0.9 dated 2017-06-22 and 0.0.1 dated 2017-06-23

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New package data.world with initial version 1.1.1
Package: data.world
Title: Main Package for Working with 'data.world' Data Sets
Version: 1.1.1
Authors@R: c( person("Rafael", "Pereira", email = "rafael.pereira@data.world", role = c("aut", "cre")), person("Triet", "Le", email = "triet.le@data.world", role = c("aut")), person("Bryon", "Jacob", email = "bryon.jacob@data.world", role = c("aut")))
Description: High-level tools for working with data.world data sets. data.world is a community where you can find interesting data, store and showcase your own data and data projects, and find and collaborate with other members. In addition to exploring, querying and charting data on the data.world site, you can access data via 'API' endpoints and integrations. Use this package to access, query and explore data sets, and to integrate data into R projects. Visit <https://data.world>, for additional information.
Depends: R (>= 3.3.0)
License: Apache License 2.0
LazyData: true
Imports: dwapi, httr, ini
Suggests: testthat, knitr, rmarkdown, readr
Encoding: UTF-8
URL: https://github.com/datadotworld/data.world-r
BugReports: https://github.com/datadotworld/data.world-r/issues
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-06-23 03:50:11 UTC; root
Author: Rafael Pereira [aut, cre], Triet Le [aut], Bryon Jacob [aut]
Maintainer: Rafael Pereira <rafael.pereira@data.world>
Repository: CRAN
Date/Publication: 2017-06-23 06:39:02 UTC

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New package dartR with initial version 0.79
Package: dartR
Type: Package
Title: Importing and Analysing Snp and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis
Version: 0.79
Date: 2017-06-23
Authors@R: c( person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), person("Arthur", "Georges", email="georges@aerg.edu.au", role="aut"), person("Peter J.", "Unmack", email="peter.mail2@unmack.net", rol="ctb"), person("Oliver", "Berry", email="oliver.berry@csiro.au", rol="ctb" ) )
Description: Functions are provided that facilitate the import and analysis of snp and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of snp and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE. Other functions are available for visualization after PCoA, or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip packages etc.
VignetteBuilder: knitr
Depends: R (>= 3.1.1), adegenet (>= 2.0.0)
Imports: plyr, tidyr, reshape2, MASS, ggplot2, directlabels, quadprog, rgl, misc3d, pca3d, utils, Demerelate, seqinr, pegas, SNPassoc, methods, doParallel, stats, data.table, parallel, foreach, stringr, ape, vegan, SNPRelate
Suggests: knitr, rmarkdown, StAMPP, mmod
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-06-23 02:36:57 UTC; s425824
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2017-06-23 06:38:33 UTC

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New package beginr with initial version 0.0.1
Package: beginr
Version: 0.0.1
Date: 2017-06-22
Title: Functions for R Beginners
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Depends: R (>= 3.1.0)
Imports:
Suggests:
Description: Useful functions for R beginners, including hints for the arguments of the 'plot()' function, self-defined functions for error bars, user-customized pair plots and hist plots, enhanced linear regression figures, etc.. This package could be helpful to R experts as well.
License: GPL
URL: https://github.com/pzhaonet/beginr
BugReports: https://github.com/pzhaonet/beginr/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-23 08:22:30 UTC; c7701105
Repository: CRAN
Date/Publication: 2017-06-23 08:49:37 UTC

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New package BCgee with initial version 0.1
Package: BCgee
Title: Bias-Corrected Estimates for Generalized Linear Models for Dependent Data
Version: 0.1
Suggests: gee
Date: 2017-06-22
Author: Nicola Lunardon <nicola.lunardon@unimib.it>, Daniel Scharfstein <dscharf@jhu.edu>
Maintainer: Nicola Lunardon <nicola.lunardon@unimib.it>
Description: Provides bias-corrected estimates for the regression coefficients of a marginal model estimated with generalized estimating equations. Details about the bias formula used are in Lunardon, N., Scharfstein, D. (2017) <doi:10.1002/sim.7366>.
License: GPL-2
Encoding: latin1
NeedsCompilation: no
Packaged: 2017-06-23 07:42:14 UTC; nicola
Repository: CRAN
Date/Publication: 2017-06-23 08:11:42 UTC

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Thu, 22 Jun 2017

Package srvyr updated to version 0.2.2 with previous version 0.2.1 dated 2017-04-26

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

Diff between srvyr versions 0.2.1 dated 2017-04-26 and 0.2.2 dated 2017-06-22

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Package survey updated to version 3.32-1 with previous version 3.32 dated 2017-06-07

Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>

Diff between survey versions 3.32 dated 2017-06-07 and 3.32-1 dated 2017-06-22

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Package IntegratedMRF updated to version 1.1.8 with previous version 1.1.5 dated 2016-08-10

Title: Integrated Prediction using Uni-Variate and Multivariate Random Forests
Description: An implementation of a framework for drug sensitivity prediction from various genetic characterizations using ensemble approaches. Random Forests or Multivariate Random Forest predictive models can be generated from each genetic characterization that are then combined using a Least Square Regression approach. It also provides options for the use of different error estimation approaches of Leave-one-out, Bootstrap, N-fold cross validation and 0.632+Bootstrap along with generation of prediction confidence interval using Jackknife-after-Bootstrap approach.
Author: Raziur Rahman, Ranadip Pal
Maintainer: Raziur Rahman <razeeebuet@gmail.com>

Diff between IntegratedMRF versions 1.1.5 dated 2016-08-10 and 1.1.8 dated 2017-06-22

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Package corpus updated to version 0.7.0 with previous version 0.6.0 dated 2017-06-06

Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, for searching for term occurrences, and for computing term occurrence frequencies (including n-grams).
Author: Patrick O. Perry [aut, cre], Martin Porter and Richard Boulton [ctb, cph] (Snowball), Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

Diff between corpus versions 0.6.0 dated 2017-06-06 and 0.7.0 dated 2017-06-22

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 corpus-0.7.0/corpus/src/termset.c                               |only
 corpus-0.7.0/corpus/src/text.c                                  |    2 
 corpus-0.7.0/corpus/src/text_locate.c                           |only
 corpus-0.7.0/corpus/src/text_nunit.c                            |only
 corpus-0.7.0/corpus/src/text_split.c                            |   58 
 corpus-0.7.0/corpus/src/text_tokens.c                           |only
 corpus-0.7.0/corpus/src/text_types.c                            |only
 corpus-0.7.0/corpus/src/util.c                                  |   21 
 corpus-0.7.0/corpus/tests/testthat/test-term_counts.R           |    2 
 corpus-0.7.0/corpus/tests/testthat/test-term_matrix.R           |   57 
 corpus-0.7.0/corpus/tests/testthat/test-text_nunit.R            |only
 corpus-0.7.0/corpus/tests/testthat/test-text_split_sentences.R  |   41 
 corpus-0.7.0/corpus/tests/testthat/test-text_tokens.R           |only
 82 files changed, 1965 insertions(+), 1650 deletions(-)

More information about corpus at CRAN
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Package templates updated to version 0.2.0 with previous version 0.1.0 dated 2017-01-07

Title: A System for Working with Templates
Description: Provides tools to work with template code and text in R. It aims to provide a simple substitution mechanism for R-expressions inside these templates. Templates can be written in other languages like 'SQL', can simply be represented by characters in R, or can themselves be R-expressions or functions.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>

Diff between templates versions 0.1.0 dated 2017-01-07 and 0.2.0 dated 2017-06-22

 DESCRIPTION                             |   10 +++++-----
 MD5                                     |   21 +++++++++++----------
 NAMESPACE                               |    1 +
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 R/NAMESPACE.R                           |    1 +
 R/helper.R                              |    6 ++++++
 R/utils.R                               |   10 +++++-----
 build/vignette.rds                      |binary
 inst/doc/Template_Programming_in_R.html |   10 +++++-----
 man/tmpl.Rd                             |    3 +--
 man/utils.Rd                            |   13 ++++++-------
 tests/testthat/test-utils.R             |   17 +++++++++++++++++
 12 files changed, 58 insertions(+), 34 deletions(-)

More information about templates at CRAN
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Package solvebio updated to version 0.4.1 with previous version 0.4.0 dated 2017-06-19

Title: The Official SolveBio API Client for R
Description: R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs. For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>

Diff between solvebio versions 0.4.0 dated 2017-06-19 and 0.4.1 dated 2017-06-22

 DESCRIPTION                               |   15 +++--
 MD5                                       |   79 +++++++++++++++---------------
 NAMESPACE                                 |    2 
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 man/Dataset.all.Rd                        |    1 
 man/Dataset.count.Rd                      |    1 
 man/Dataset.create.Rd                     |    1 
 man/Dataset.data.Rd                       |    1 
 man/Dataset.facets.Rd                     |    1 
 man/Dataset.get_or_create_by_full_name.Rd |    1 
 man/Dataset.query.Rd                      |    1 
 man/Dataset.retrieve.Rd                   |    1 
 man/DatasetCommit.all.Rd                  |    1 
 man/DatasetCommit.retrieve.Rd             |    1 
 man/DatasetExport.all.Rd                  |    1 
 man/DatasetExport.create.Rd               |    1 
 man/DatasetExport.retrieve.Rd             |    1 
 man/DatasetField.all.Rd                   |    1 
 man/DatasetField.create.Rd                |    1 
 man/DatasetField.facets.Rd                |    1 
 man/DatasetField.retrieve.Rd              |    1 
 man/DatasetImport.all.Rd                  |    1 
 man/DatasetImport.create.Rd               |    1 
 man/DatasetImport.retrieve.Rd             |    1 
 man/DatasetMigration.all.Rd               |    1 
 man/DatasetMigration.create.Rd            |    1 
 man/DatasetMigration.retrieve.Rd          |    1 
 man/Depository.all.Rd                     |    1 
 man/Depository.create.Rd                  |    1 
 man/Depository.latest_version.Rd          |    1 
 man/Depository.retrieve.Rd                |    1 
 man/Depository.versions.Rd                |    1 
 man/DepositoryVersion.all.Rd              |    1 
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 man/DepositoryVersion.datasets.Rd         |    1 
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 man/Upload.all.Rd                         |    1 
 man/Upload.create.Rd                      |    1 
 man/Upload.retrieve.Rd                    |    1 
 man/login.Rd                              |    1 
 42 files changed, 51 insertions(+), 81 deletions(-)

More information about solvebio at CRAN
Permanent link


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