Sun, 22 Jul 2018

Package sparr updated to version 2.2-12 with previous version 2.2-11 dated 2018-03-10

Title: Spatial and Spatiotemporal Relative Risk
Description: Provides functions to estimate kernel-smoothed spatial and spatio-temporal densities and relative risk functions, and perform subsequent inference. Methodological details can be found in the accompanying tutorial: Davies et al. (2018) <DOI:10.1002/sim.7577>.
Author: Tilman M. Davies [aut, cre], Jonathan C. Marshall [aut]
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>

Diff between sparr versions 2.2-11 dated 2018-03-10 and 2.2-12 dated 2018-07-22

 DESCRIPTION                          |    8 ++--
 MD5                                  |   64 +++++++++++++++++------------------
 NEWS                                 |   10 +++++
 R/LSCV.density.R                     |    2 -
 R/LSCV.risk.R                        |    2 -
 R/SLIK.adapt.R                       |   21 +++++++----
 R/bivariate.density.R                |    2 -
 R/bivden.LOO.R                       |    4 +-
 R/fft.R                              |    2 -
 R/multiscale.density.R               |    2 -
 R/multiscale.slice.R                 |    2 -
 R/plot.bivden.R                      |    2 -
 R/plot.stden.R                       |    2 +
 R/spattemp.slice.R                   |    2 -
 R/tolerance.R                        |    2 -
 README.md                            |    2 -
 man/BOOT.density.Rd                  |    2 -
 man/BOOT.spattemp.Rd                 |    4 +-
 man/CV.Rd                            |    2 -
 man/LSCV.risk.Rd                     |    2 -
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 man/bivariate.density.Rd             |    2 -
 man/fft2d.Rd                         |    2 -
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 man/multiscale.density.Rd            |    2 -
 man/multiscale.slice.Rd              |    2 -
 man/plotsparr.Rd                     |    2 -
 man/sparr-package.Rd                 |    4 +-
 man/spattemp.density.Rd              |    2 -
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 man/tolerance.Rd                     |    2 -
 33 files changed, 101 insertions(+), 78 deletions(-)

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Sat, 21 Jul 2018

New package wdman with initial version 0.2.4
Package: wdman
Type: Package
Title: 'Webdriver'/'Selenium' Binary Manager
Version: 0.2.4
Authors@R: c( person("John", "Harrison", , "johndharrison0@gmail.com", role = "aut", comment = "original author"), person("Ju Yeong", "Kim", , "jkim2345@fredhutch.org", role = "cre", comment = "rOpenSci maintainer"))
Description: There are a number of binary files associated with the 'Webdriver'/'Selenium' project (see <http://www.seleniumhq.org/download/>, <https://sites.google.com/a/chromium.org/chromedriver/>, <https://github.com/mozilla/geckodriver>, <http://phantomjs.org/download.html> and <https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver> for more information). This package provides functions to download these binaries and to manage processes involving them.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2)
Suggests: testthat, covr, knitr, rmarkdown
Imports: binman, assertthat, subprocess (>= 0.8.0), yaml, semver(>= 0.2.0), utils
URL: https://github.com/ropensci/wdman
URLNote: https://github.com/ropensci/wdman
BugReports: https://github.com/ropensci/wdman/issues
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-21 17:32:38 UTC; jkim
Author: John Harrison [aut] (original author), Ju Yeong Kim [cre] (rOpenSci maintainer)
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>
Repository: CRAN
Date/Publication: 2018-07-21 21:50:03 UTC

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Package statnetWeb updated to version 0.5.0 with previous version 0.4.0 dated 2015-11-05

Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet' software.
Author: Martina Morris [cre, aut], Emily Beylerian [aut], Kirk Li [ctb], Samuel Jenness [ctb]
Maintainer: Martina Morris <morrism@uw.edu>

Diff between statnetWeb versions 0.4.0 dated 2015-11-05 and 0.5.0 dated 2018-07-21

 statnetWeb-0.4.0/statnetWeb/man/run_sw.Rd              |only
 statnetWeb-0.5.0/statnetWeb/DESCRIPTION                |   22 
 statnetWeb-0.5.0/statnetWeb/MD5                        |   28 
 statnetWeb-0.5.0/statnetWeb/NAMESPACE                  |   46 
 statnetWeb-0.5.0/statnetWeb/R/run_sw.R                 |   32 
 statnetWeb-0.5.0/statnetWeb/R/statnetWeb-package.R     |   56 
 statnetWeb-0.5.0/statnetWeb/README.md                  |   62 
 statnetWeb-0.5.0/statnetWeb/inst/shiny/global.R        |  336 
 statnetWeb-0.5.0/statnetWeb/inst/shiny/server.R        | 7684 ++++-----
 statnetWeb-0.5.0/statnetWeb/inst/shiny/ui.R            | 2798 +--
 statnetWeb-0.5.0/statnetWeb/inst/shiny/www/alert.js    |  490 
 statnetWeb-0.5.0/statnetWeb/inst/shiny/www/busy.js     |   28 
 statnetWeb-0.5.0/statnetWeb/inst/shiny/www/mycosmo.css |13462 ++++++++---------
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Package scclust updated to version 0.1.2 with previous version 0.1.1 dated 2017-05-22

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

Diff between scclust versions 0.1.1 dated 2017-05-22 and 0.1.2 dated 2018-07-21

 DESCRIPTION             |   14 +++++++-------
 MD5                     |    6 +++---
 NEWS.md                 |    5 +++++
 tests/testthat/config.R |    3 +++
 4 files changed, 18 insertions(+), 10 deletions(-)

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Package quickmatch updated to version 0.1.3 with previous version 0.1.2 dated 2017-05-20

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

Diff between quickmatch versions 0.1.2 dated 2017-05-20 and 0.1.3 dated 2018-07-21

 DESCRIPTION                              |   14 +++++++-------
 MD5                                      |   26 +++++++++++++++-----------
 NAMESPACE                                |    1 +
 NEWS.md                                  |only
 R/covariate_averages.R                   |only
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 R/lm_match.R                             |    2 +-
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 README.md                                |   30 ++++++++++++++++++++++++------
 man/covariate_averages.Rd                |only
 man/lm_match.Rd                          |    2 +-
 man/matching_weights.Rd                  |    2 +-
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 tests/testthat/test_covariate_averages.R |only
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 16 files changed, 90 insertions(+), 56 deletions(-)

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Package ggpval updated to version 0.2.1 with previous version 0.2.0 dated 2017-07-26

Title: Annotate Statistical Tests for 'ggplot2'
Description: Automatically performs desired statistical tests (e.g. wilcox.test(), t.test()) to compare between groups, and adds the resulting p-values to the plot with an annotation bar. Visualizing group differences are frequently performed by boxplots, bar plots, etc. Statistical test results are often needed to be annotated on these plots. This package provides a convenient function that works on 'ggplot2' objects, performs the desired statistical test between groups of interest and annotates the test results on the plot.
Author: Jun Cheng [aut, cre]
Maintainer: Jun Cheng <s6juncheng@gmail.com>

Diff between ggpval versions 0.2.0 dated 2017-07-26 and 0.2.1 dated 2018-07-21

 ggpval-0.2.0/ggpval/tests/test-add_pval.R |only
 ggpval-0.2.1/ggpval/DESCRIPTION           |    8 ++++----
 ggpval-0.2.1/ggpval/MD5                   |   11 ++++++-----
 ggpval-0.2.1/ggpval/R/add_pval_ggplot.R   |   30 ++++++++++++++++++------------
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 ggpval-0.2.1/ggpval/inst/doc/ggpval.html  |   12 ++++++------
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 8 files changed, 34 insertions(+), 27 deletions(-)

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Package ClusterR updated to version 1.1.3 with previous version 1.1.2 dated 2018-05-06

Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans and K-Medoids Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans and k-medoids clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between ClusterR versions 1.1.2 dated 2018-05-06 and 1.1.3 dated 2018-07-21

 DESCRIPTION                        |    8 ++++----
 MD5                                |   20 ++++++++++----------
 NEWS.md                            |    5 +++++
 R/clustering_functions.R           |   12 ++++++------
 README.md                          |    3 ++-
 inst/doc/the_clusterR_package.html |   12 ++++++------
 man/KMeans_rcpp.Rd                 |    4 ++--
 man/MiniBatchKmeans.Rd             |    2 +-
 man/Optimal_Clusters_KMeans.Rd     |    2 +-
 man/external_validation.Rd         |    2 +-
 man/predict_KMeans.Rd              |    2 +-
 11 files changed, 39 insertions(+), 33 deletions(-)

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Package geojsonR updated to version 1.0.5 with previous version 1.0.4 dated 2017-11-30

Title: A GeoJson Processing Toolkit
Description: Includes functions for processing GeoJson objects <https://en.wikipedia.org/wiki/GeoJSON> relying on 'RFC 7946' <https://tools.ietf.org/pdf/rfc7946.pdf>. The geojson encoding is based on 'json11', a tiny JSON library for 'C++11' <https://github.com/dropbox/json11>. Furthermore, the source code is exported in R through the 'Rcpp' and 'RcppArmadillo' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between geojsonR versions 1.0.4 dated 2017-11-30 and 1.0.5 dated 2018-07-21

 DESCRIPTION                        |    8 ++++----
 MD5                                |   14 +++++++-------
 NEWS.md                            |    5 +++++
 R/utils.R                          |    8 ++++----
 README.md                          |    3 ++-
 build/vignette.rds                 |binary
 inst/doc/the_geojsonR_package.html |    4 ++--
 man/shiny_from_JSON.Rd             |    2 +-
 8 files changed, 25 insertions(+), 19 deletions(-)

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Package elmNNRcpp updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-05

Title: The Extreme Learning Machine Algorithm
Description: Training and predict functions for Single Hidden-layer Feedforward Neural Networks (SLFN) using the Extreme Learning Machine (ELM) algorithm. The ELM algorithm differs from the traditional gradient-based algorithms for very short training times (it doesn't need any iterative tuning, this makes learning time very fast) and there is no need to set any other parameters like learning rate, momentum, epochs, etc. This is a reimplementation of the 'elmNN' package using 'RcppArmadillo' after the 'elmNN' package was archived. For more information, see "Extreme learning machine: Theory and applications" by Guang-Bin Huang, Qin-Yu Zhu, Chee-Kheong Siew (2006), Elsevier B.V, <doi:10.1016/j.neucom.2005.12.126>.
Author: Lampros Mouselimis [aut, cre], Alberto Gosso [aut]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between elmNNRcpp versions 1.0.0 dated 2018-07-05 and 1.0.1 dated 2018-07-21

 DESCRIPTION                            |   10 ++-
 MD5                                    |   16 ++---
 NEWS.md                                |    4 +
 README.md                              |   15 +++++
 inst/doc/extreme_learning_machine.R    |   85 +++++++++++++++++++++-------
 inst/doc/extreme_learning_machine.Rmd  |   89 +++++++++++++++++++++---------
 inst/doc/extreme_learning_machine.html |   97 +++++++++++++++++++++++----------
 src/init.c                             |    2 
 vignettes/extreme_learning_machine.Rmd |   89 +++++++++++++++++++++---------
 9 files changed, 291 insertions(+), 116 deletions(-)

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Package BAMBI updated to version 2.0.1 with previous version 2.0.0 dated 2018-06-21

Title: Bivariate Angular Mixture Models
Description: Fit (using Bayesian methods) and simulate mixtures of univariate and bivariate angular distributions. Chakraborty and Wong (2017) <arXiv:1708.07804> .
Author: Saptarshi Chakraborty, Samuel W.K. Wong
Maintainer: Saptarshi Chakraborty <chakra.saptarshi@gmail.com>

Diff between BAMBI versions 2.0.0 dated 2018-06-21 and 2.0.1 dated 2018-07-21

 DESCRIPTION       |   11 ++++++-----
 MD5               |    8 ++++----
 NAMESPACE         |    1 +
 R/fit_mixmodel.R  |   19 ++++++++++---------
 man/fit_angmix.Rd |    2 +-
 5 files changed, 22 insertions(+), 19 deletions(-)

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Package nmslibR updated to version 1.0.3 with previous version 1.0.2 dated 2018-05-10

Title: Non Metric Space (Approximate) Library
Description: A Non-Metric Space Library ('NMSLIB' <https://github.com/searchivarius/nmslib>) wrapper, which according to the authors "is an efficient cross-platform similarity search library and a toolkit for evaluation of similarity search methods. The goal of the 'NMSLIB' <https://github.com/searchivarius/nmslib> Library is to create an effective and comprehensive toolkit for searching in generic non-metric spaces. Being comprehensive is important, because no single method is likely to be sufficient in all cases. Also note that exact solutions are hardly efficient in high dimensions and/or non-metric spaces. Hence, the main focus is on approximate methods". The wrapper also includes Approximate Kernel k-Nearest-Neighbor functions based on the 'NMSLIB' <https://github.com/searchivarius/nmslib> 'Python' Library.
Author: Lampros Mouselimis [aut, cre], B. Naidan [cph] (Author of the Non-Metric Space Library (NMSLIB)), L. Boytsov [cph] (Author of the Non-Metric Space Library (NMSLIB)), Yu. Malkov [cph] (Author of the Non-Metric Space Library (NMSLIB)), B. Frederickson [cph] (Author of the Non-Metric Space Library (NMSLIB)), D. Novak [cph] (Author of the Non-Metric Space Library (NMSLIB))
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

Diff between nmslibR versions 1.0.2 dated 2018-05-10 and 1.0.3 dated 2018-07-21

 DESCRIPTION                       |    8 +--
 MD5                               |    8 +--
 NEWS.md                           |    4 +
 README.md                         |   84 +++++++++++++++++++-------------------
 inst/doc/the_nmslibR_package.html |    4 -
 5 files changed, 57 insertions(+), 51 deletions(-)

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Package semds updated to version 0.9-5 with previous version 0.9-4 dated 2018-06-14

Title: Structural Equation Multidimensional Scaling
Description: Fits a structural equation multidimensional scaling (SEMDS) model for asymmetric and three-way input dissimilarities. It assumes that the dissimilarities are measured with errors. The latent dissimilarities are estimated as factor scores within an SEM framework while the objects are represented in a low-dimensional space as in MDS.
Author: Patrick Mair [aut, cre], Jose Fernando Vera [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

Diff between semds versions 0.9-4 dated 2018-06-14 and 0.9-5 dated 2018-07-21

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New package rda with initial version 1.0.2-2.1
Package: rda
Version: 1.0.2-2.1
Date: 2012-06-30
Title: Shrunken Centroids Regularized Discriminant Analysis
Author: Yaqian Guo <yaqiang@stat.stanford.edu> Trevor Hastie <hastie@stat.stanford.edu> Robert Tibshirani <tibs@stanford.edu>
Maintainer: ORPHANED
Depends: R (>= 2.10)
Description: Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.
License: GPL (>= 2)
Packaged: 2018-07-21 16:59:24 UTC; hornik
Repository: CRAN
Date/Publication: 2018-07-21 17:12:01 UTC
NeedsCompilation: no
X-CRAN-Original-Maintainer: Rob Tibshirani <tibs@stanford.edu>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package plsdof with initial version 0.2-7.1
Package: plsdof
Type: Package
Title: Degrees of Freedom and Statistical Inference for Partial Least Squares Regression
Depends: MASS
Version: 0.2-7.1
Date: 2014-09-04
Author: Nicole Kraemer, Mikio L. Braun
Maintainer: ORPHANED
Description: The plsdof package provides Degrees of Freedom estimates for Partial Least Squares (PLS) Regression. Model selection for PLS is based on various information criteria (aic, bic, gmdl) or on cross-validation. Estimates for the mean and covariance of the PLS regression coefficients are available. They allow the construction of approximate confidence intervals and the application of test procedures. Further, cross-validation procedures for Ridge Regression and Principal Components Regression are available.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2018-07-21 16:59:31 UTC; hornik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-07-21 17:11:59 UTC
X-CRAN-Original-Maintainer: Nicole Kraemer <kraemer_r_packages@yahoo.de>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package penalizedSVM with initial version 1.1.1
Package: penalizedSVM
Type: Package
Title: Feature Selection SVM using Penalty Functions
Version: 1.1.1
Date: 2010-08-02
Depends: e1071, MASS, corpcor, statmod, tgp, mlegp, lhs
Author: Natalia Becker, Wiebke Werft, Axel Benner
Maintainer: ORPHANED
Description: Provides feature selection SVM using penalty functions. The smoothly clipped absolute deviation (SCAD), 'L1-norm', 'Elastic Net' ('L1-norm' and 'L2-norm') and 'Elastic SCAD' (SCAD and 'L2-norm') penalties are available. The tuning parameters can be found using either a fixed grid or a interval search.
License: GPL (>= 2)
LazyLoad: yes
Encoding: latin1
Packaged: 2018-07-21 17:04:21 UTC; hornik
Repository: CRAN
Date/Publication: 2018-07-21 17:11:57 UTC
NeedsCompilation: no
X-CRAN-Original-Maintainer: Natalia Becker <natalia.becker@dkfz.de>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package diffusionMap with initial version 1.1-0.1
Package: diffusionMap
Version: 1.1-0.1
Date: 2014-02-19
Title: Diffusion Map
Author: Joseph Richards <joeyrichar@gmail.com>
Maintainer: ORPHANED
Description: Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model.
Depends: R (>= 2.4.0)
Imports: scatterplot3d, igraph, Matrix
License: GPL-2
URL: http://www.stat.berkeley.edu/~jwrichar/software.html
Packaged: 2018-07-21 17:16:50 UTC; hornik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-07-21 17:26:23 UTC
X-CRAN-Original-Maintainer: Joseph Richards <joeyrichar@gmail.com>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package cleandata with initial version 0.1.0
Package: cleandata
Type: Package
Title: Functions to Inspect, Impute, and Encode Data, and to Keep Track of This Process
Version: 0.1.0
Author: Sherry Zhao
Maintainer: Sherry Zhao <sxzhao@gwu.edu>
Description: Functions to work with data frames to prepare data further analysis. The functions for imputation and encoding can produce log files to keep track of data manipulation process.
BugReports: https://github.com/sherrisherry/cleandata/issues
Depends: R (>= 3.0.0)
Imports: stats
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-07-17 22:58:52 UTC; Admin
Repository: CRAN
Date/Publication: 2018-07-21 18:00:03 UTC

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New package c060 with initial version 0.2-4
Package: c060
Version: 0.2-4
Date: 2014-12-09
Author: Martin Sill, Thomas Hielscher, Manuela Zucknick, Natalia Becker.
Maintainer: Martin Sill <m.sill@dkfz.de>
Title: Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models
Depends:
Imports: glmnet, survival, parallel, mlegp, tgp, peperr, penalizedSVM, lattice
Suggests:
Description: c060 provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models
License: GPL-2
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: c060
Repository/R-Forge/Revision: 185
Repository/R-Forge/DateTimeStamp: 2014-12-11 13:09:54
Date/Publication: 2014-12-11 17:04:38
Packaged: 2014-12-11 13:30:10 UTC; rforge
NeedsCompilation: no

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Package nngeo updated to version 0.2.1 with previous version 0.2.0 dated 2018-07-18

Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C implementation of the Vincenty Formula for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers.
Author: Michael Dorman [aut, cre], Johnathan Rush [ctb], Ian Hough [ctb], Jan Antala [ctb, cph] (Author of C code for Vincenty distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between nngeo versions 0.2.0 dated 2018-07-18 and 0.2.1 dated 2018-07-21

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 nngeo-0.2.1/nngeo/NEWS.md            |    6 +++++-
 nngeo-0.2.1/nngeo/build/vignette.rds |binary
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 8 files changed, 13 insertions(+), 12 deletions(-)

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Package mpath updated to version 0.3-5 with previous version 0.3-4 dated 2017-10-23

Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty. See Wang et al. (2014) <doi:10.1002/sim.6314>, Wang et al. (2015) <doi:10.1002/bimj.201400143>, Wang et al. (2016) <doi:10.1177/0962280214530608>.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>

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Package dtwclust updated to version 5.5.0 with previous version 5.4.1 dated 2018-06-10

Title: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Description: Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>

Diff between dtwclust versions 5.4.1 dated 2018-06-10 and 5.5.0 dated 2018-07-21

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Package compound.Cox updated to version 3.14 with previous version 3.13 dated 2018-07-12

Title: Univariate Feature Selection and Compound Covariate for Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions). Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>, statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>, Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2018-)<to appear>. Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between compound.Cox versions 3.13 dated 2018-07-12 and 3.14 dated 2018-07-21

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Package R.devices updated to version 2.16.0 with previous version 2.15.1 dated 2016-11-10

Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.devices versions 2.15.1 dated 2016-11-10 and 2.16.0 dated 2018-07-21

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 R.devices-2.16.0/R.devices/NEWS                                                                                     | 1391 ++++---
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 R.devices-2.16.0/R.devices/R/eps.R                                                                                  |   20 
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 R.devices-2.16.0/R.devices/tests/dataURI.R                                                                          |   36 
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 R.devices-2.16.0/R.devices/tests/devEqualTypes.R                                                                    |    4 
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 R.devices-2.16.0/R.devices/tests/devIsOpen.R                                                                        |   28 
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 R.devices-2.16.0/R.devices/tests/devListIndexOf.R                                                                   |   30 
 R.devices-2.16.0/R.devices/tests/devSet.R                                                                           |  128 
 R.devices-2.16.0/R.devices/tests/devTypeName.R                                                                      |   84 
 R.devices-2.16.0/R.devices/tests/withPar.R                                                                          |  100 
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Package multistateutils updated to version 1.2.0 with previous version 1.1.0 dated 2018-06-17

Title: Utility Functions for Parametric Multi-State Models
Description: Provides functions for working with multi-state modelling, such as efficient simulation routines for estimating transition probabilities and length of stay. It is designed as an extension to multi-state modelling capabilities provided with the 'flexsurv' package (see Jackson (2016) <doi:10.18637/jss.v070.i08>).
Author: Stuart Lacy
Maintainer: Stuart Lacy <stuart.lacy@gmail.com>

Diff between multistateutils versions 1.1.0 dated 2018-06-17 and 1.2.0 dated 2018-07-21

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Package spagmix updated to version 0.3-0 with previous version 0.2-0 dated 2018-07-02

Title: Artificial Spatial and Spatiotemporal Densities on Bounded Windows
Description: A utility package containing some simple tools to design and generate density functions on bounded regions in space and space-time, and simulate iid data therefrom. See Davies & Hazelton (2010) <doi:10.1002/sim.3995> for example.
Author: Anna K. Redmond and Tilman M. Davies
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>

Diff between spagmix versions 0.2-0 dated 2018-07-02 and 0.3-0 dated 2018-07-21

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Package CBCgrps updated to version 2.2 with previous version 2.1 dated 2017-08-16

Title: Compare Baseline Characteristics Between Groups
Description: Compare baseline characteristics between two or more groups. The variables being compared can be factor and numeric variables. The function will automatically judge the type and distribution of the variables, and make statistical description and bivariate analysis.
Author: Zhongheng Zhang, Sir Run-Run Shaw hospital, Zhejiang university school of medicine
Maintainer: Zhongheng Zhang <zh_zhang1984@zju.edu.cn>

Diff between CBCgrps versions 2.1 dated 2017-08-16 and 2.2 dated 2018-07-21

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Package dlookr updated to version 0.3.2 with previous version 0.3.0 dated 2018-04-27

Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation. Data diagnostics provides information and visualization of missing values and outliers and unique and negative values to help you understand the distribution and quality of your data. Data exploration provides information and visualization of the descriptive statistics of univariate variables, normality tests and outliers, correlation of two variables, and relationship between target variable and predictor. Data transformation supports binning for categorizing continuous variables, imputates missing values and outliers, resolving skewness. And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>

Diff between dlookr versions 0.3.0 dated 2018-04-27 and 0.3.2 dated 2018-07-21

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Fri, 20 Jul 2018

Package summarytools updated to version 0.8.6 with previous version 0.8.5 dated 2018-06-17

Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Author: Dominic Comtois
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>

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Package redland updated to version 1.0.17-10 with previous version 1.0.17-9 dated 2016-12-14

Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <http://www.w3.org/TR/rdf-primer>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Jeroen Ooms [aut], Carl Boettiger [aut], Scott Chamberlain [aut], David Beckett [cph], University of Bristol [cph], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>

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Package FKF updated to version 0.1.5 with previous version 0.1.4 dated 2018-07-13

Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman filter, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in BLAS and LAPACK. Due to the speed of the filter, the fitting of high-dimensional linear state space models to large datasets becomes possible. This package also contains a plot function for the visualization of the state vector and graphical diagnostics of the residuals.
Author: David Luethi, Philipp Erb, Simon Otziger
Maintainer: Paul Smith <paul@waternumbers.co.uk>

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Package distances updated to version 0.1.3 with previous version 0.1.2 dated 2017-05-23

Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

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Package brms updated to version 2.4.0 with previous version 2.3.1 dated 2018-06-05

Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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New package TDAstats with initial version 0.1.0
Package: TDAstats
Type: Package
Title: Pipeline for Topological Data Analysis
Version: 0.1.0
Authors@R: c( person("Raoul", "Wadhwa", email = "raoulwadhwa@gmail.com", role = c("aut", "cre")), person("Andrew", "Dhawan", role = "aut"), person("Drew", "Williamson", role = "aut"), person("Jacob", "Scott", role = "aut"))
Description: A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: ggplot2 (>= 2.2.1), Rcpp (>= 0.12.15)
URL: https://github.com/rrrlw/TDAstats
BugReports: https://github.com/rrrlw/TDAstats/issues
LinkingTo: Rcpp
RoxygenNote: 6.0.1
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2018-07-20 16:46:18 UTC; rrrlw
Author: Raoul Wadhwa [aut, cre], Andrew Dhawan [aut], Drew Williamson [aut], Jacob Scott [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 17:50:02 UTC

More information about TDAstats at CRAN
Permanent link

Package stringi updated to version 1.2.4 with previous version 1.2.3 dated 2018-06-12

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

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 configure              |   61 +++++++++++++++++++++++++++++++++++++++++++++----
 man/stri_isempty.Rd    |    3 --
 man/stri_length.Rd     |    5 +---
 man/stri_numbytes.Rd   |    3 --
 man/stri_width.Rd      |    1 
 src/icu61/data         |only
 src/uconfig_local.h.in |   12 +++++++++
 12 files changed, 108 insertions(+), 53 deletions(-)

More information about stringi at CRAN
Permanent link

New package SpNetPrep with initial version 1.0
Package: SpNetPrep
Title: Linear Network Preprocessing for Spatial Statistics
Version: 1.0
Author: Alvaro Briz-Redon
Maintainer: Alvaro Briz-Redon <alvaro.briz@uv.es>
Description: Launches a Shiny application that allows users to carry out some of the steps that are required to curate both a linear network object based on a road structure and a point pattern that lies on such a network, becoming two previous steps to the performance of a spatial statistics analysis.
Depends: R (>= 3.5.0)
License: GPL-2
Imports: spatstat, leaflet, shiny, sp, raster, maptools
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2018-07-20 15:47:37 UTC; Alvaro
Repository: CRAN
Date/Publication: 2018-07-20 18:00:07 UTC

More information about SpNetPrep at CRAN
Permanent link

Package sampler updated to version 0.2.2 with previous version 0.2.0 dated 2018-05-31

Title: Sample Design, Drawing & Data Analysis Using Data Frames
Description: Determine sample sizes, draw samples, and conduct data analysis using data frames. It specifically enables you to determine simple random sample sizes, stratified sample sizes, and complex stratified sample sizes using a secondary variable such as population; draw simple random samples and stratified random samples from sampling data frames; determine which observations are missing from a random sample, missing by strata, duplicated within a dataset; and perform data analysis, including proportions, margins of error and upper and lower bounds for simple, stratified and cluster sample designs.
Author: Michael Baldassaro
Maintainer: Michael Baldassaro <mbaldassaro@gmail.com>

Diff between sampler versions 0.2.0 dated 2018-05-31 and 0.2.2 dated 2018-07-20

 DESCRIPTION  |    8 -
 MD5          |   12 +-
 NAMESPACE    |    3 
 R/sampler.R  |    2 
 R/ssamp.R    |   14 +-
 README.md    |  304 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 man/ssamp.Rd |    3 
 7 files changed, 322 insertions(+), 24 deletions(-)

More information about sampler at CRAN
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New package rhierbaps with initial version 1.0.0
Package: rhierbaps
Type: Package
Title: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Version: 1.0.0
Authors@R: person("Gerry", "Tonkin-Hill", email = "g.tonkinhill@gmail.com", role = c("cre", "aut"))
Description: Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ape, dplyr, purrr, utils, ggplot2, LambertW
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, ggtree, phytools, testthat
VignetteBuilder: knitr
URL: https://github.com/gtonkinhill/rhierbaps
BugReports: https://github.com/gtonkinhill/rhierbaps/issues
NeedsCompilation: no
Packaged: 2018-07-16 22:36:58 UTC; gt4
Author: Gerry Tonkin-Hill [cre, aut]
Maintainer: Gerry Tonkin-Hill <g.tonkinhill@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 18:00:03 UTC

More information about rhierbaps at CRAN
Permanent link

Package Rfast updated to version 1.9.1 with previous version 1.9.0 dated 2018-05-14

Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <papadakm95@gmail.com>

Diff between Rfast versions 1.9.0 dated 2018-05-14 and 1.9.1 dated 2018-07-20

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Package plotly updated to version 4.8.0 with previous version 4.7.1 dated 2017-07-29

Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Chris Parmer [aut], Toby Hocking [aut], Scott Chamberlain [aut], Karthik Ram [aut], Marianne Corvellec [aut], Pedro Despouy [aut], Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>

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Package WVPlots updated to version 1.0.2 with previous version 1.0.1 dated 2018-07-11

Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'. Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions, conditioned scatter plot with marginal densities, box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package simmer updated to version 4.0.0 with previous version 3.8.0 dated 2018-05-01

Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation (DES) package for R. It is designed as a generic yet powerful framework. The architecture encloses a robust and fast simulation core written in 'C++' with automatic monitoring capabilities. It provides a rich and flexible R API that revolves around the concept of trajectory, a common path in the simulation model for entities of the same type.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>), Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>

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Package lazy updated to version 1.2-16 with previous version 1.2-15 dated 2013-09-22

Title: Lazy Learning for Local Regression
Description: By combining constant, linear, and quadratic local models, lazy estimates the value of an unknown multivariate function on the basis of a set of possibly noisy samples of the function itself. This implementation of lazy learning automatically adjusts the bandwidth on a query-by-query basis through a leave-one-out cross-validation.
Author: Mauro Birattari <mbiro@ulb.ac.be> and Gianluca Bontempi <gbonte@ulb.ac.be>
Maintainer: Gianluca Bontempi <gbonte@ulb.ac.be>

Diff between lazy versions 1.2-15 dated 2013-09-22 and 1.2-16 dated 2018-07-20

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Package arsenal updated to version 1.3.0 with previous version 1.2.0 dated 2018-04-16

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

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More information about arsenal at CRAN
Permanent link

Package vtreat updated to version 1.3.0 with previous version 1.2.3 dated 2018-07-11

Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. 'vtreat' prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new categorical levels (levels seen during application, but not during training). Reference: "'vtreat': a data.frame Processor for Predictive Modeling", 'Zumel', 'Mount', 2016, DOI:10.5281/zenodo.1173314.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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More information about vtreat at CRAN
Permanent link

Package spind updated to version 2.2.0 with previous version 2.1.3 dated 2018-04-08

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>

Diff between spind versions 2.1.3 dated 2018-04-08 and 2.2.0 dated 2018-07-20

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New package spatsoc with initial version 0.1.0
Package: spatsoc
Title: Group Animal Relocation Data by Spatial and Temporal Relationship
Version: 0.1.0
Authors@R: c( person("Alec L.", "Robitaille", role = c("aut", "cre"), email = "robit.alec@gmail.com"), person("Quinn", "Webber", role = c("aut")), person("Eric", "Vander Wal", role = c("aut")) )
Description: Detects spatial and temporal groups in GPS relocations. It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks. In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.
Depends: R (>= 3.4)
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: data.table (>= 1.10.5), sp, rgeos, adehabitatHR, igraph, methods
Suggests: testthat, knitr, rmarkdown
SystemRequirements: GEOS (>= 3.2.0)
RoxygenNote: 6.0.1
VignetteBuilder: knitr
BugReports: https://www.gitlab.com/robit.a/spatsoc/issues
URL: https://spatsoc.gitlab.io
NeedsCompilation: no
Packaged: 2018-07-20 15:26:41 UTC; alecr
Author: Alec L. Robitaille [aut, cre], Quinn Webber [aut], Eric Vander Wal [aut]
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 16:00:02 UTC

More information about spatsoc at CRAN
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Package seplyr updated to version 0.5.9 with previous version 0.5.7 dated 2018-06-30

Title: Improved Standard Evaluation Interfaces for Common Data Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved standard evaluation adapter methods for important common 'dplyr' data manipulation tasks. In addition the 'seplyr' package supplies several new "key operations bound together" methods. These include 'group_summarize()' (which combines grouping, arranging and calculation in an atomic unit), 'add_group_summaries()' (which joins grouped summaries into a 'data.frame' in a well documented manner), 'add_group_indices()' (which adds per-group identifiers to a 'data.frame' without depending on row-order), 'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()' (which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between seplyr versions 0.5.7 dated 2018-06-30 and 0.5.9 dated 2018-07-20

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More information about seplyr at CRAN
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Package replyr updated to version 0.9.7 with previous version 0.9.6 dated 2018-06-23

Title: Patches to Use 'dplyr' on Remote Data Sources
Description: Patches to use 'dplyr' on remote data sources ('SQL' databases, 'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning user code works similarly on all such sources, without needing per-source adaption). Due to the fluctuating nature of 'dplyr'/'dbplyr'/'rlang' 'APIs' this package is going into maintenance mode. Most of the 'replyr' functions are already done better by one of the non-monolithic replacement packages: 'wrapr', 'seplyr', 'rquery', or 'cdata'.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between replyr versions 0.9.6 dated 2018-06-23 and 0.9.7 dated 2018-07-20

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More information about replyr at CRAN
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New package MortalityGaps with initial version 1.0.0
Package: MortalityGaps
Type: Package
Title: The Double-Gap Life Expectancy Forecasting Model
Version: 1.0.0
Authors@R: c( person("Marius D.", "Pascariu", role = c("aut", "cre"), email = "rpascariu@outlook.com"))
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Description: Life expectancy is highly correlated over time among countries and between males and females. These associations can be used to improve forecasts. Here we have implemented a method for forecasting female life expectancy based on analysis of the gap between female life expectancy in a country compared with the record level of female life expectancy in the world. Second, to forecast male life expectancy, the gap between male life expectancy and female life expectancy in a country is analysed. We named this method the Double-Gap model. For a detailed description of the method see Pascariu et al. (2017). <doi:10.1016/j.insmatheco.2017.09.011>.
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.1.2)
Imports: forecast, MASS, crch, pbapply
Suggests: knitr, rmarkdown, testthat, covr
RoxygenNote: 6.0.1
VignetteBuilder: knitr
URL: https://github.com/mpascariu/MortalityGaps
BugReports: https://github.com/mpascariu/MortalityGaps/issues
NeedsCompilation: no
Packaged: 2018-07-17 04:24:01 UTC; mpascariu
Author: Marius D. Pascariu [aut, cre]
Repository: CRAN
Date/Publication: 2018-07-20 15:20:09 UTC

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New package gifski with initial version 0.8.3
Package: gifski
Type: Package
Title: Highest Quality GIF Encoder
Version: 0.8.3
Authors@R: c( person("Jeroen", "Ooms", ,"jeroen@berkeley.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4035-0289")), person("Kornel Lesiński", role = "cph", comment = "Gifski Rust library"))
Description: Multi-threaded GIF encoder written in Rust: <https://gif.ski/>. Converts images to GIF animations using pngquant's efficient cross-frame palettes and temporal dithering with thousands of colors per frame.
License: MIT + file LICENSE
URL: https://gif.ski/ (upstream), https://github.com/r-rust/gifski (devel)
BugReports: https://github.com/r-rust/gifski/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: ggplot2, gapminder
Language: en-US
NeedsCompilation: yes
Packaged: 2018-07-20 14:30:03 UTC; jeroen
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Kornel Lesiński [cph] (Gifski Rust library)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Repository: CRAN
Date/Publication: 2018-07-20 15:10:03 UTC

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Package cdata updated to version 0.7.3 with previous version 0.7.2 dated 2018-07-07

Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 . Based on the 'DBI' database interface.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between cdata versions 0.7.2 dated 2018-07-07 and 0.7.3 dated 2018-07-20

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New package anyLib with initial version 1.0.4
Package: anyLib
Type: Package
Title: Install and Load Any Package from CRAN, Bioconductor or Github
Version: 1.0.4
Authors@R: c(person("Aurelien", "Chateigner", role = c("aut", "cre"), email = "aurelien.chateigner@gmail.com"))
Description: Made to make your life simpler with packages, by installing and loading a list of packages, whether they are on CRAN, Bioconductor or github. For github, if you do not have the full path, with the maintainer name in it (e.g. "achateigner/topReviGO"), it will be able to load it but not to install it.
License: CC BY-SA 4.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
biocViews:
Imports: devtools, withr, BiocInstaller, httr, curl
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-17 11:34:27 UTC; achateigner
Author: Aurelien Chateigner [aut, cre]
Maintainer: Aurelien Chateigner <aurelien.chateigner@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 15:20:07 UTC

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New package wilson with initial version 2.0.1
Package: wilson
Type: Package
Title: Web-Based Interactive Omics Visualization
Version: 2.0.1
Authors@R: c( person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")), person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"), person("Looso", "Mario", email = "mario.looso@mpi-bn.mpg.de", role = "aut"))
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
URL: https://github.molgen.mpg.de/loosolab/wilson/
BugReports: https://github.molgen.mpg.de/loosolab/wilson/issues/
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: shiny, data.table, ggplot2, plotly, scales, shinydashboard, DT (>= 0.3), colourpicker, RColorBrewer, shinyjs, viridis, rje, grDevices, grid, plyr, circlize, ComplexHeatmap, stats, gplots, reshape, rintrojs, RJSONIO, ggrepel (>= 0.6.12), DESeq2, rjson, FactoMineR, factoextra, heatmaply (>= 0.14.1), shinycssloaders, log4r, openssl, methods, R6
RoxygenNote: 6.0.1
biocViews:
Suggests: knitr, rmarkdown, testthat, vdiffr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-16 14:00:19 UTC; hschult
Author: Hendrik Schultheis [aut, cre], Jens Preussner [aut], Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>
Repository: CRAN
Date/Publication: 2018-07-20 15:00:02 UTC

More information about wilson at CRAN
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Package uGMAR updated to version 2.0.3 with previous version 2.0.2 dated 2018-07-05

Title: Estimate Univariate Gaussian or Student's t Mixture Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR), Student's t Mixture Autoregressive (StMAR) and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models, quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes. Also general linear constraints and restricting autoregressive parameters to be the same for all regimes are supported. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>, Leena Kalliovirta (2012) <doi:10.1111/j.1368-423X.2011.00364.x>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>

Diff between uGMAR versions 2.0.2 dated 2018-07-05 and 2.0.3 dated 2018-07-20

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 R/argumentChecks.R                          |  815 +++++++++----------
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 R/getOmega.R                                |  163 ++-
 R/loglikelihood.R                           | 1174 ++++++++++++++--------------
 R/parameterReforms.R                        |  654 +++++++--------
 R/plotGMAR.R                                |  291 +++---
 R/quantileResidualTests.R                   |  426 +++++-----
 R/quantileResiduals.R                       |  166 +--
 R/simulateGMAR.R                            |  158 +--
 inst/doc/intro-to-uGMAR.html                |    4 
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 man/loglikelihood.Rd                        |    2 
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 man/simulateGMAR.Rd                         |    3 
 man/standardErrors.Rd                       |    2 
 tests/testthat/test_GAfunctions.R           |  200 ++--
 tests/testthat/test_getOmega.R              |  284 +++---
 tests/testthat/test_quantileResidualTests.R |  166 +--
 tests/testthat/test_quantileResiduals.R     |  130 +--
 24 files changed, 3043 insertions(+), 3033 deletions(-)

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New package spp with initial version 1.15.5
Package: spp
Type: Package
Title: ChIP-Seq Processing Pipeline
Version: 1.15.5
Author: Peter K
Date: 2018-07-19
Depends: R (>= 3.3.0), Rcpp
Imports: Rsamtools, caTools, parallel, graphics, stats
Suggests: methods
LinkingTo: Rcpp, BH (>= 1.66)
OS_type: unix
Maintainer: Peter Kharchenko <spppackage.maintenance@gmail.com>
Description: Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) <DOI:10.1038/nbt.1508>].
License: GPL-2
LazyLoad: yes
Note: revised for compliance with CRAN by K.Pal and C.M.Livi
NeedsCompilation: yes
Packaged: 2018-07-20 14:33:02 UTC; clivi
Repository: CRAN
Date/Publication: 2018-07-20 14:50:02 UTC

More information about spp at CRAN
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New package SODC with initial version 1.0
Package: SODC
Type: Package
Title: Optimal Discriminant Clustering(ODC) and Sparse Optimal Discriminant Clustering(SODC)
Version: 1.0
Date: 2013-05-15
Author: Yanhong Wang
Maintainer: Yanhong Wang <wangyanhongws@gmail.com>
Description: To implement two clustering methods, ODC and SODC, for clustering datasets using optimal scoring, can also be used as an dimension reduction tool.
License: GPL-2
Depends: magic,ppls,psych,MASS
Packaged: 2013-05-23 13:34:01 UTC; matyxwx
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-23 15:53:52

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New package ppls with initial version 1.6-1.1
Package: ppls
Type: Package
Title: Penalized Partial Least Squares
Depends: R (>= 2.10), splines, MASS
Version: 1.6-1.1
Date: 2014-09-04
Author: Nicole Kraemer <kraemer_r_packages@yahoo.de> Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>
Maintainer: ORPHANED
Description: Contains linear and nonlinear regression methods based on Partial Least Squares and Penalization Techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.
License: GPL (>= 2)
Packaged: 2018-07-20 14:33:03 UTC; hornik
Repository: CRAN
NeedsCompilation: no
Date/Publication: 2018-07-20 14:38:39 UTC
X-CRAN-Original-Maintainer: Nicole Kraemer <kraemer_r_packages@yahoo.de>
X-CRAN-Comment: Orphaned and corrected on 2018-07-20 as check problems were not corrected despite reminders.

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New package parcor with initial version 0.2-6
Package: parcor
Type: Package
Title: Regularized estimation of partial correlation matrices
Version: 0.2-6
Date: 2014-09-04
Depends: MASS, glmnet, ppls, Epi, GeneNet
Author: Nicole Kraemer, Juliane Schaefer
Maintainer: Nicole Kraemer <kraemer_r_packages@yahoo.de>
Description: The package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-09-04 08:54:12 UTC; ga29xul
Repository: CRAN
NeedsCompilation: no
Date/Publication: 2014-09-04 13:43:30

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New package clustRcompaR with initial version 0.2.0
Package: clustRcompaR
Type: Package
Title: Easy Interface for Clustering a Set of Documents and Exploring Group- Based Patterns
Version: 0.2.0
Date: 2018-01-23
Author: Joshua Rosenberg, Alex Lishinski
Maintainer: Alex Lishinski <alexlishinski@gmail.com>
Description: Provides an interface to perform cluster analysis on a corpus of text. Interfaces to Quanteda to assemble text corpuses easily. Deviationalizes text vectors prior to clustering using technique described by Sherin (Sherin, B. [2013]. A computational study of commonsense science: An exploration in the automated analysis of clinical interview data. Journal of the Learning Sciences, 22(4), 600-638. Chicago. <doi:10.1080/10508406.2013.836654>). Uses cosine similarity as distance metric for two stage clustering process, involving Ward's algorithm hierarchical agglomerative clustering, and k-means clustering. Selects optimal number of clusters to maximize "variance explained" by clusters, adjusted by the number of clusters. Provides plotted output of clustering results as well as printed output. Assesses "model fit" of clustering solution to a set of preexisting groups in dataset.
License: GPL-3
Depends: R (>= 3.1.3),
URL: https://github.com/alishinski/clustRcompaR
Imports: quanteda, dplyr, ggplot2, ppls
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
LazyData: true
NeedsCompilation: no
Packaged: 2018-01-28 19:56:04 UTC; alex
Repository: CRAN
Date/Publication: 2018-01-28 21:04:49

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New package calibrateBinary with initial version 0.1
Package: calibrateBinary
Type: Package
Title: Calibration for Computer Experiments with Binary Responses
Version: 0.1
Date: 2018-07-16
Author: Chih-Li Sung
Maintainer: Chih-Li Sung <iamdfchile@gmail.com>
Description: Performs the calibration procedure proposed by Sung et al. (2018+) <arXiv:1806.01453>. This calibration method is particularly useful when the outputs of both computer and physical experiments are binary and the estimation for the calibration parameters is of interest.
License: GPL-2 | GPL-3
RoxygenNote: 5.0.1
Depends: R (>= 2.14.1)
Imports: GPfit, gelnet, kernlab, randtoolbox
NeedsCompilation: no
Packaged: 2018-07-16 05:40:08 UTC; apple
Repository: CRAN
Date/Publication: 2018-07-20 15:00:07 UTC

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New package POCRE with initial version 0.5.0
Package: POCRE
Title: Penalized Orthogonal-Components Regression
Version: 0.5.0
Date: 2018-07-15
Author: Dabao Zhang, Zhongli Jiang, Zeyu Zhang
Maintainer: Dabao Zhang <zhangdb@purdue.edu>
Description: Penalized orthogonal-components regression (POCRE) is a supervised dimension reduction method for high-dimensional data. It sequentially constructs orthogonal components (with selected features) which are maximally correlated to the response residuals. POCRE can also construct common components for multiple responses and thus build up latent-variable models.
Imports: stats,utils,ggplot2 (>= 2.2.0),pracma,EbayesThresh
License: GPL-2
NeedsCompilation: no
Packaged: 2018-07-15 05:07:10 UTC; admin-zhangdb
Repository: CRAN
Date/Publication: 2018-07-20 13:20:03 UTC

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New package jstor with initial version 0.3.2
Package: jstor
Title: Read Data from JSTOR/DfR
Version: 0.3.2
Authors@R: person("Thomas", "Klebel", email = "t.klebel@hotmail.com", role = c("aut", "cre"))
Description: Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR.
Depends: R (>= 3.1)
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr (>= 0.7.4), tidyr (>= 0.7.2), purrr (>= 0.2.4), xml2 (>= 1.2.0), magrittr, stringr (>= 1.3.0), readr (>= 1.0.0), tibble (>= 1.4.1), rlang (>= 0.2.0), furrr (>= 0.1.0), readxl (>= 1.0.0), curl, pryr
Suggests: testthat, covr, knitr, rmarkdown, future
BugReports: https://github.com/ropensci/jstor/issues
URL: https://github.com/ropensci/jstor, https://ropensci.github.io/jstor/
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-15 12:50:00 UTC; tklebel
Author: Thomas Klebel [aut, cre]
Maintainer: Thomas Klebel <t.klebel@hotmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 13:30:03 UTC

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Package trimcluster updated to version 0.1-2.1 with previous version 0.1-2 dated 2007-11-05

Title: Cluster Analysis with Trimming
Description: Trimmed k-means clustering.
Author: Christian Hennig <chrish@stats.ucl.ac.uk>
Maintainer: ORPHANED

Diff between trimcluster versions 0.1-2 dated 2007-11-05 and 0.1-2.1 dated 2018-07-20

 DESCRIPTION    |   18 ++++++++++++------
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 NAMESPACE      |only
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 4 files changed, 14 insertions(+), 10 deletions(-)

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Package spant updated to version 0.11.0 with previous version 0.10.0 dated 2018-06-25

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data.
Author: Martin Wilson [cre, aut], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

Diff between spant versions 0.10.0 dated 2018-06-25 and 0.11.0 dated 2018-07-20

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Package fpc updated to version 2.1-11.1 with previous version 2.1-11 dated 2018-01-12

Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
Author: Christian Hennig <c.hennig@ucl.ac.uk>
Maintainer: ORPHANED

Diff between fpc versions 2.1-11 dated 2018-01-12 and 2.1-11.1 dated 2018-07-20

 DESCRIPTION |   11 +++++++----
 MD5         |    4 ++--
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 3 files changed, 10 insertions(+), 7 deletions(-)

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Package caTools updated to version 1.17.1.1 with previous version 1.17.1 dated 2014-09-10

Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
Description: Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
Author: Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>
Maintainer: ORPHANED

Diff between caTools versions 1.17.1 dated 2014-09-10 and 1.17.1.1 dated 2018-07-20

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Package BALCONY updated to version 0.2.8 with previous version 0.2.7 dated 2018-06-07

Title: Better ALignment CONsensus analYsis
Description: Facilitates the evolutionary analysis and structure conservation study of specified amino acids in proteins.
Author: Michal Stolarczyk & Alicja Pluciennik
Maintainer: Michal Stolarczyk <stolarczyk.michal93@gmail.com>

Diff between BALCONY versions 0.2.7 dated 2018-06-07 and 0.2.8 dated 2018-07-20

 DESCRIPTION                      |    6 
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Package SPUTNIK updated to version 1.0.3.1 with previous version 1.0.2 dated 2018-03-30

Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>

Diff between SPUTNIK versions 1.0.2 dated 2018-03-30 and 1.0.3.1 dated 2018-07-20

 DESCRIPTION       |   10 -
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 5 files changed, 515 insertions(+), 494 deletions(-)

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Package insect updated to version 1.1.1 with previous version 1.1.0 dated 2018-06-24

Title: Informatic Sequence Classification Trees
Description: Provides a bioinformatics pipeline for DNA meta-barcoding analysis, including functions for sequence parsing, demultiplexing, quality filtering and probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>

Diff between insect versions 1.1.0 dated 2018-06-24 and 1.1.1 dated 2018-07-20

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Package ggstance updated to version 0.3.1 with previous version 0.3 dated 2016-11-16

Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components: horizontal versions of 'Stats' and 'Geoms', and vertical versions of 'Positions'.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], Winston Chang [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between ggstance versions 0.3 dated 2016-11-16 and 0.3.1 dated 2018-07-20

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Package forestControl updated to version 0.2.0 with previous version 0.1.1 dated 2018-02-19

Title: Approximate False Positive Rate Control in Selection Frequency for Random Forest
Description: Approximate false positive rate control in selection frequency for random forest using the methods described by Ender Konukoglu and Melanie Ganz (2014) <arXiv:1410.2838>. Methods for calculating the selection frequency threshold at false positive rates and selection frequency false positive rate feature selection.
Author: Tom Wilson [aut, cre], Jasen Finch [aut]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>

Diff between forestControl versions 0.1.1 dated 2018-02-19 and 0.2.0 dated 2018-07-20

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New package rcheology with initial version 3.5.1.0
Package: rcheology
Version: 3.5.1.0
Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 2.0.0 onwards.
Authors@R: person("David", "Hugh-Jones", , "davidhughjones@gmail.com", c("aut", "cre"))
License: CC0
URL: https://github.com/hughjonesd/rcheology
BugReports: https://github.com/hughjonesd/rcheology/issues
Depends: R(>= 2.10)
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2018-07-13 21:42:25 UTC; david
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 09:50:03 UTC

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New package polyPK with initial version 3.1.0
Package: polyPK
Type: Package
Title: The Pharmacokinetics (PK) of Multi-Component Drugs Using a Metabolomics Approach
Version: 3.1.0
Author: Mengci Li, Shouli Wang, Guoxiang Xie, Tianlu Chen and Wei Jia
Maintainer: Tianlu Chen <chentianlu@sjtu.edu.cn>
Description: Poly-PK strategy is a new strategy of pharmacokinetic analysis of multi-component drugs (Guoxiang Xie, Tianlu Chen, Wei Jia, et al. (2012)<doi:10.1021/pr300318m>; Ke Lan, Guoxiang Xie and Wei Jia. (2013)<doi:10.1155/2013/819147>). This package is the first implementation of the Poly-PK strategy with 10 easy-to-use functions.
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Imports: imputeLCMD,plyr,sqldf,gplots,corrplot,circlize,mixOmics,pkr,Hmisc,ropls
Depends: impute,pcaMethods,xlsx
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-11 06:39:00 UTC; limengci
Repository: CRAN
Date/Publication: 2018-07-11 07:30:06 UTC

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New package openVA with initial version 1.0.5
Package: openVA
Type: Package
Title: Automated Method for Verbal Autopsy
Version: 1.0.5
Date: 2018-07-06
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Depends: R (>= 3.4.0)
Imports: InterVA5 (>= 1.0.1), InSilicoVA (>= 1.1.3), InterVA4 (>= 1.7.3), Tariff (>= 1.0.1), ggplot2, crayon, cli, purrr
Suggests: nbc4va
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
License: GPL-2
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-07 05:07:51 UTC; zehangli
Repository: CRAN
Date/Publication: 2018-07-07 16:20:08 UTC

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Package foreign updated to version 0.8-71 with previous version 0.8-70.2 dated 2018-07-18

Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>

Diff between foreign versions 0.8-70.2 dated 2018-07-18 and 0.8-71 dated 2018-07-20

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Package BNSP updated to version 2.0.7 with previous version 2.0.6 dated 2018-06-12

Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for variable selection in mean/variance regression models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>

Diff between BNSP versions 2.0.6 dated 2018-06-12 and 2.0.7 dated 2018-07-20

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Package ppls (with last version 1.6-1) was removed from CRAN

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

2014-09-04 1.6-1
2013-08-20 1.6-0
2013-07-25 1.5.1
2011-04-27 1.05
2009-11-12 1.04
2009-01-24 1.03
2008-07-08 1.02
2008-04-15 1.01
2007-10-07 1.0

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Package samr (with last version 2.0) was removed from CRAN

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2011-06-29 2.0
2010-03-13 1.28
2010-01-04 1.27
2008-09-28 1.26
2007-06-07 1.25

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Package sparcl (with last version 1.0.3) was removed from CRAN

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2013-01-04 1.0.3
2011-12-07 1.0.2
2010-05-16 1.0.1
2009-12-02 1.0

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2017-03-03 1.0.0

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2012-07-02 1.0.2-2
2012-06-30 1.0.2-1
2009-04-29 1.0.2
2009-03-01 1.0.1
2006-02-14 1.0

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Package lumberjack updated to version 0.3.0 with previous version 0.2.0 dated 2017-08-08

Title: Track Changes in Data
Description: A function composition ('pipe') operator and extensible framework that allows for easy logging of changes in data.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

Diff between lumberjack versions 0.2.0 dated 2017-08-08 and 0.3.0 dated 2018-07-20

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New package ggvoronoi with initial version 0.8.0
Package: ggvoronoi
Version: 0.8.0
Date: 2018-07-14
Title: Voronoi Diagrams and Heatmaps with 'ggplot2'
Author: Robert C. Garrett [aut, cre], Austin Nar [aut], Thomas J. Fisher [aut]
Maintainer: Robert C. Garrett <garretrc@miamioh.edu>
Authors@R: c(person("Robert C.", "Garrett", email = "garretrc@miamioh.edu", role = c("aut", "cre")), person("Austin", "Nar", email = "narar@miamioh.edu", role = c("aut")), person("Thomas J.", "Fisher", email = "fishert4@miamioh.edu", role = c("aut")))
Description: Easy creation and manipulation of Voronoi diagrams using 'deldir' with visualization in 'ggplot2'.
Depends: R (>= 2.10), ggplot2 (>= 2.2.0)
Imports: deldir, sp, rgeos, raster, methods
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: knitr, rmarkdown, ggmap, dplyr, scales
VignetteBuilder: knitr
URL: https://github.com/garretrc/ggvoronoi/
NeedsCompilation: no
Packaged: 2018-07-14 20:12:30 UTC; garretrc
Repository: CRAN
Date/Publication: 2018-07-20 08:20:06 UTC

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Package c060 (with last version 0.2-4) was removed from CRAN

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

2014-12-11 0.2-4
2014-01-22 0.2-3
2013-04-16 0.2

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Package imputeR (with last version 2.0) was removed from CRAN

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Package penalizedSVM (with last version 1.1) was removed from CRAN

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2010-08-23 1.1
2009-01-14 1.0

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Package openVA (with last version 1.0.5) was removed from CRAN

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2018-07-07 1.0.5
2018-05-16 1.0.4
2017-01-07 1.0.3
2016-11-19 1.0.2
2016-03-28 1.0.1
2016-03-12 1.0

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Package nbc4va (with last version 1.0) was removed from CRAN

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2016-07-11 1.0

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Package parcor (with last version 0.2-6) was removed from CRAN

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2014-09-04 0.2-6
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Package BPEC (with last version 1.2.1) was removed from CRAN

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2018-04-03 1.2.1
2018-03-22 1.2
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2016-04-06 1.0

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Package LncPath (with last version 1.0) was removed from CRAN

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2016-05-16 1.0

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Package eLNNpaired (with last version 0.2.3) was removed from CRAN

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2017-04-09 0.2.3

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2010-07-24 1.0-3
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Package SparseLearner (with last version 1.0-2) was removed from CRAN

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2015-11-17 1.0-2
2015-10-13 1.0.1
2015-10-10 1.0

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Package GPPFourier (with last version 2.1) was removed from CRAN

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2017-09-22 2.1

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Package R2G2 (with last version 1.0-2) was removed from CRAN

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2013-04-23 1.0-2
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Package plsdof (with last version 0.2-7) was removed from CRAN

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2014-09-04 0.2-7
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2012-07-26 0.2-3
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Package diffusionMap (with last version 1.1-0) was removed from CRAN

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Package polyPK (with last version 3.1.0) was removed from CRAN

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2018-07-11 3.1.0
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Package mFilter (with last version 0.1-3) was removed from CRAN

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

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2018-01-28 0.2.0
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Package plsRbeta (with last version 0.2.2) was removed from CRAN

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2018-06-11 0.2.2
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Package SODC (with last version 1.0) was removed from CRAN

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2013-05-23 1.0

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Package vagalumeR updated to version 0.1.3 with previous version 0.1.1 dated 2017-10-08

Title: Access to the 'Vagalume' API
Description: Provides access to the 'Vagalume' API <https://api.vagalume.com.br>. The data extracted is basically lyrics of songs and information about artists/bands.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>

Diff between vagalumeR versions 0.1.1 dated 2017-10-08 and 0.1.3 dated 2018-07-20

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Package spm updated to version 1.1.1 with previous version 1.1.0 dated 2018-03-20

Title: Spatial Predictive Modeling
Description: Introduction to some novel accurate hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. It contains two commonly used geostatistical methods, two machine learning methods, four hybrid methods and two averaging methods. For each method, two functions are provided. One function is for assessing the predictive errors and accuracy of the method based on cross-validation. The other one is for generating spatial predictions using the method. For details please see: Li, J., Potter, A., Huang, Z., Daniell, J. J. and Heap, A. (2010) <https:www.ga.gov.au/metadata-gateway/metadata/record/gcat_71407> Li, J., Heap, A. D., Potter, A., Huang, Z. and Daniell, J. (2011) <doi:10.1016/j.csr.2011.05.015> Li, J., Heap, A. D., Potter, A. and Daniell, J. (2011) <doi:10.1016/j.envsoft.2011.07.004> Li, J., Potter, A., Huang, Z. and Heap, A. (2012) <https:www.ga.gov.au/metadata-gateway/metadata/record/74030>.
Author: Jin Li [aut, cre]
Maintainer: Jin Li <jin.li@ga.gov.au>

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Package gam updated to version 1.16 with previous version 1.15 dated 2018-02-25

Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between gam versions 1.15 dated 2018-02-25 and 1.16 dated 2018-07-20

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Thu, 19 Jul 2018

Package NonCompart updated to version 0.4.4 with previous version 0.4.3 dated 2018-06-21

Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) Use of CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package ncar updated to version 0.4.1 with previous version 0.4.0 dated 2018-06-20

Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method 5) Produce pdf, rtf, text report files. * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package tkrplot updated to version 0.0-24 with previous version 0.0-23 dated 2011-11-19

Title: TK Rplot
Description: Simple mechanism for placing R graphics in a Tk widget.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>

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Package rredlist updated to version 0.5.0 with previous version 0.4.0 dated 2017-08-26

Title: 'IUCN' Red List Client
Description: 'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Author: Scott Chamberlain [aut, cre], rOpenSci [fnd] (https://ropensci.org/), Maëlle Salmon [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package robustbase updated to version 0.93-1.1 with previous version 0.93-1 dated 2018-06-23

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre], Peter Rousseeuw [ctb] (Qn and Sn), Christophe Croux [ctb] (Qn and Sn), Valentin Todorov [aut] (most robust Cov), Andreas Ruckstuhl [aut] (nlrob, anova, glmrob), Matias Salibian-Barrera [aut] (lmrob orig.), Tobias Verbeke [ctb, fnd] (mc, adjbox), Manuel Koller [aut] (mc, lmrob, psi-func.), Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob), Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package RcppParallel updated to version 4.4.1 with previous version 4.4.0 dated 2018-03-02

Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut], Romain Francois [aut, cph], Kevin Ushey [aut, cre], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/), RStudio [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>

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Package GWASinlps updated to version 1.2 with previous version 1.1 dated 2018-02-02

Title: Nonlocal Prior Based Iterative SNP Selection Tool for Genome-Wide Association Studies
Description: Performs variable selection with data from Genome-wide association studies (GWAS) combining, in an iterative variable selection framework, the computational efficiency of the screen-and-select approach based on some association learning and the parsimonious uncertainty quantification provided by the use of nonlocal priors, as described in Sanyal et al. (2018).
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nilotpal.sanyal@gmail.com>

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Package blastula updated to version 0.2.1 with previous version 0.2.0 dated 2018-03-27

Title: Easily Send HTML Email Messages
Description: Compose and send out responsive HTML email messages that render perfectly across a range of email clients and device sizes. Messages are composed using 'Markdown' and a text interpolation system that allows for the injection of evaluated R code within the message body, footer, and subject line. Helper functions let the user insert embedded images, web link buttons, and 'ggplot2' plot objects into the message body. Messages can be sent through an 'SMTP' server or through the 'Mailgun' API service <http://mailgun.com/>.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>)
Maintainer: Richard Iannone <riannone@me.com>

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Package npsf updated to version 0.4.1 with previous version 0.3.1 dated 2018-01-17

Title: Nonparametric and Stochastic Efficiency and Productivity Analysis
Description: Provides a variety of tools for nonparametric and parametric efficiency measurement.
Author: Oleg Badunenko [aut, cre], Yaryna Kolomiytseva [aut], Pavlo Mozharovskyi [aut]
Maintainer: Oleg Badunenko <oleg.badunenko@port.ac.uk>

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Package sigr updated to version 0.2.8 with previous version 0.2.7 dated 2018-07-03

Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting and planning of experimental results, working around issue such as the difficulty of extracting model summary facts (such as with 'lm'/'glm'). This package also includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package serieslcb updated to version 0.2.0 with previous version 0.1.0 dated 2018-07-01

Title: Lower Confidence Bounds for Binomial Series System
Description: Calculate lower confidence bounds for binomial series system reliability. The R 'shiny' application, launched by launch_app(), weaves together a workflow of customized simulations and delta coverage calculations to output recommended lower confidence bound methods.
Author: Edward Schuberg
Maintainer: Edward Schuberg <eschu003@ucr.edu>

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Package rpart.plot updated to version 3.0.1 with previous version 3.0.0 dated 2018-07-12

Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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 rpart.plot-3.0.1/rpart.plot/tests/test.rpart.plot.R                   |   12 
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More information about rpart.plot at CRAN
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Package tmvmixnorm updated to version 1.0.2 with previous version 1.0.1 dated 2018-07-18

Title: Sampling from Truncated Multivariate Normal and t Distributions
Description: Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong. Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributions. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multivariate Student's t distribution is also developed. Moreover, the proposed method and computation remain valid for high dimensional and strong dependence scenarios. Empirical results in Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> illustrated the superior performance in terms of various criteria (e.g. mixing and integrated auto-correlation time).
Author: Ting Fung (Ralph) Ma [cre, aut], Sujit K. Ghosh [aut], Yifang Li [aut]
Maintainer: Ting Fung (Ralph) Ma <tingfung.ma@wisc.edu>

Diff between tmvmixnorm versions 1.0.1 dated 2018-07-18 and 1.0.2 dated 2018-07-19

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Package timeseriesdb updated to version 0.4 with previous version 0.2.1 dated 2015-04-04

Title: Manage Time Series for Official Statistics with R and PostgreSQL
Description: Archive and manage times series data from official statistics. The 'timeseriesdb' package was designed to manage a large catalog of time series from official statistics which are typically published on a monthly, quarterly or yearly basis. Thus timeseriesdb is optimized to handle updates caused by data revision as well as elaborate, multi-lingual meta information.
Author: "Matthias Bannert <bannert@kof.ethz.ch> [aut, cre]"
Maintainer: 'Matthias Bannert' <bannert@kof.ethz.ch>

Diff between timeseriesdb versions 0.2.1 dated 2015-04-04 and 0.4 dated 2018-07-19

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More information about timeseriesdb at CRAN
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Package table1 updated to version 1.1 with previous version 1.0 dated 2018-04-26

Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect to see as the first table (i.e. "Table 1") in a medical/epidemiological journal article.
Author: Benjamin Rich [aut, cre]
Maintainer: Benjamin Rich <mail@benjaminrich.net>

Diff between table1 versions 1.0 dated 2018-04-26 and 1.1 dated 2018-07-19

 DESCRIPTION                   |   13 
 MD5                           |   29 
 NAMESPACE                     |    5 
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 18 files changed, 2565 insertions(+), 2883 deletions(-)

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Package logistf updated to version 1.23 with previous version 1.22 dated 2016-12-19

Title: Firth's Bias-Reduced Logistic Regression
Description: Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal solution to the problem of separation in logistic regression. If needed, the bias reduction can be turned off such that ordinary maximum likelihood logistic regression is obtained.
Author: Georg Heinze [aut, cre], Meinhard Ploner [aut], Daniela Dunkler [ctb], Harry Southworth [ctb]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>

Diff between logistf versions 1.22 dated 2016-12-19 and 1.23 dated 2018-07-19

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Package HydeNet updated to version 0.10.8 with previous version 0.10.7 dated 2018-01-02

Title: Hybrid Bayesian Networks Using R and JAGS
Description: Facilities for easy implementation of hybrid Bayesian networks using R. Bayesian networks are directed acyclic graphs representing joint probability distributions, where each node represents a random variable and each edge represents conditionality. The full joint distribution is therefore factorized as a product of conditional densities, where each node is assumed to be independent of its non-descendents given information on its parent nodes. Since exact, closed-form algorithms are computationally burdensome for inference within hybrid networks that contain a combination of continuous and discrete nodes, particle-based approximation techniques like Markov Chain Monte Carlo are popular. We provide a user-friendly interface to constructing these networks and running inference using the 'rjags' package. Econometric analyses (maximum expected utility under competing policies, value of information) involving decision and utility nodes are also supported.
Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>

Diff between HydeNet versions 0.10.7 dated 2018-01-02 and 0.10.8 dated 2018-07-19

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More information about HydeNet at CRAN
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New package happytime with initial version 0.1.0
Package: happytime
Type: Package
Title: Two Games to Relieve the Boredom
Version: 0.1.0
Author: Xiuwen Wang
Maintainer: Xiuwen Wang <wangxw36@mail2.sysu.edu.cn>
Description: There are two interesting games in this package, one is 2048 games(for windows), using up and down to control the direction until there is a 2048 figure. And the other is 'what to eat today',preparing for people who choose difficulties, including most of the delicious Cantonese cuisine.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-13 08:24:47 UTC; Administrator
Repository: CRAN
Date/Publication: 2018-07-19 17:10:03 UTC

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New package gmat with initial version 0.1.0
Package: gmat
Type: Package
Title: Simulation of Graphically Constrained Matrices
Version: 0.1.0
Date: 2018-07-13
Encoding: UTF-8
Authors@R: c( person(given = "Irene", family = "Córdoba", email = "irene.cordoba@upm.es", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3252-4234")), person(given = "Gherardo", family = "Varando", role = "aut", comment = c(ORCID = "0000-0002-6708-1103")), person(given = "Concha", family = "Bielza", role = "ths", comment = c(ORCID = "0000-0001-7109-2668")), person(given = "Pedro", family = "Larrañaga", role = "ths", comment = c(ORCID = "0000-0003-0652-9872")))
Description: Implementation of the simulation method for Gaussian graphical models described in Córdoba et al. (2018) <arXiv:1807.03090>. The package also provides an alternative method based on diagonally dominant matrices.
License: GPL (>= 2)
RoxygenNote: 6.0.1
ByteCompile: true
URL: https://github.com/irenecrsn/gmat
BugReports: https://github.com/irenecrsn/gmat/issues
Suggests: testthat
Imports: igraph, methods, stats
NeedsCompilation: yes
Packaged: 2018-07-13 09:30:46 UTC; irene
Author: Irene Córdoba [aut, cre] (<https://orcid.org/0000-0002-3252-4234>), Gherardo Varando [aut] (<https://orcid.org/0000-0002-6708-1103>), Concha Bielza [ths] (<https://orcid.org/0000-0001-7109-2668>), Pedro Larrañaga [ths] (<https://orcid.org/0000-0003-0652-9872>)
Maintainer: Irene Córdoba <irene.cordoba@upm.es>
Repository: CRAN
Date/Publication: 2018-07-19 17:20:03 UTC

More information about gmat at CRAN
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Package excursions updated to version 2.4.1 with previous version 2.3.3 dated 2018-04-03

Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055> and Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>. These can be generated by the citation function in R.
Author: David Bolin [cre, aut], Finn Lindgren [aut]
Maintainer: David Bolin <davidbolin@gmail.com>

Diff between excursions versions 2.3.3 dated 2018-04-03 and 2.4.1 dated 2018-07-19

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 excursions-2.4.1/excursions/src/qinv.cpp                          |    5 
 excursions-2.4.1/excursions/tests/testthat/helper-data.R          |   42 +
 excursions-2.4.1/excursions/tests/testthat/test.contourmap.R      |   12 
 excursions-2.4.1/excursions/tests/testthat/test.contourmap.inla.R |   62 ++
 excursions-2.4.1/excursions/tests/testthat/test.excursions.R      |    1 
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 45 files changed, 2890 insertions(+), 1209 deletions(-)

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Package dbhydroR updated to version 0.2-6 with previous version 0.2-5 dated 2018-05-22

Title: 'DBHYDRO' Hydrologic and Water Quality Data
Description: Client for programmatic access to the South Florida Water Management District's 'DBHYDRO' database at <https://www.sfwmd.gov/science-data/dbhydro>, with functions for accessing hydrologic and water quality data.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>

Diff between dbhydroR versions 0.2-5 dated 2018-05-22 and 0.2-6 dated 2018-07-19

 DESCRIPTION            |    8 ++++----
 MD5                    |   18 +++++++++---------
 NEWS.md                |    6 ++++++
 R/dbhydro_clean.R      |   22 +++++++++++-----------
 R/dbhydro_get.R        |   24 +++++++++++++-----------
 build/vignette.rds     |binary
 inst/doc/dbhydroR.Rmd  |    4 ++--
 inst/doc/dbhydroR.html |    8 ++++----
 man/get_wq.Rd          |    4 ++--
 vignettes/dbhydroR.Rmd |    4 ++--
 10 files changed, 53 insertions(+), 45 deletions(-)

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New package CKLRT with initial version 0.2.2
Package: CKLRT
Type: Package
Title: Composite Kernel Machine Regression Based on Likelihood Ratio Test
Version: 0.2.2
Author: Ni Zhao [aut], Haoyu Zhang [aut,cre]
Maintainer: Haoyu Zhang <andrew.haoyu@gmail.com>
Description: Composite Kernel Machine Regression based on Likelihood Ratio Test (CKLRT): in this package, we develop a kernel machine regression framework to model the overall genetic effect of a SNP-set, considering the possible GE interaction. Specifically, we use a composite kernel to specify the overall genetic effect via a nonparametric function and we model additional covariates parametrically within the regression framework. The composite kernel is constructed as a weighted average of two kernels, one corresponding to the genetic main effect and one corresponding to the GE interaction effect. We propose a likelihood ratio test (LRT) and a restricted likelihood ratio test (RLRT) for statistical significance. We derive a Monte Carlo approach for the finite sample distributions of LRT and RLRT statistics. (N. Zhao, H. Zhang, J. Clark, A. Maity, M. Wu. Composite Kernel Machine Regression based on Likelihood Ratio Test with Application for Combined Genetic and Gene-environment Interaction Effect (Submitted).)
License: GPL-3
Depends: R (>= 3.1.0),
Imports: Rcpp (>= 0.12.17), mgcv, MASS, nlme, compiler, stats
LinkingTo: RcppEigen, Rcpp
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-07-13 19:20:33 UTC; zhangh24
Repository: CRAN
Date/Publication: 2018-07-19 17:40:13 UTC

More information about CKLRT at CRAN
Permanent link

New package tranSurv with initial version 1.1.6
Package: tranSurv
Title: Estimating a Survival Distribution in the Presence of Dependent Left Truncation and Right Censoring
Version: 1.1.6
Authors@R: person("Sy Han (Steven)", "Chiou", email = "schiou@utdallas.edu", role = c("aut", "cre"))
Description: A structural transformation model for a latent, quasi-independent truncation time as a function of the observed dependent truncation time and the event time, and an unknown dependence parameter. The dependence parameter is chosen to minimize the conditional Kendall's tau (Martin and Betensky, 2005) <doi:10.1198/016214504000001538>. The marginal distribution for the truncation time and the event time are completely left unspecified.
License: GPL (>= 3)
URL: http://github.com/stc04003/tranSurv
BugReports: http://github.com/stc04003/tranSurv/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: survival, SQUAREM, rootSolve
Suggests: copula
NeedsCompilation: yes
Packaged: 2018-07-19 04:17:42 UTC; schiou
Author: Sy Han (Steven) Chiou [aut, cre]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Repository: CRAN
Date/Publication: 2018-07-19 17:00:02 UTC

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Package mlmm.gwas updated to version 1.0.4 with previous version 1.0.3 dated 2018-05-06

Title: Pipeline for GWAS Using MLMM
Description: Pipeline for Genome-Wide Association Study using Multi-Locus Mixed Model from Segura V, Vilhjálmsson BJ et al. (2012) <doi:10.1038/ng.2314>. The pipeline include detection of associated SNPs with MLMM, model selection by lowest eBIC, estimation of the effects of the SNPs in the selected model and graphical functions.
Author: Fanny Bonnafous [aut], Alexandra Duhnen [aut], Louise Gody [aut], Olivier Guillaume[aut, cre], Brigitte Mangin [aut], Prune Pegot-Espagnet [aut], Vincent Segura [aut], Bjarni J. Vilhjalmsson [aut]
Maintainer: Olivier Guillaume <olivier.guillaume45@gmail.com>

Diff between mlmm.gwas versions 1.0.3 dated 2018-05-06 and 1.0.4 dated 2018-07-19

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More information about mlmm.gwas at CRAN
Permanent link

Package sdmpredictors updated to version 0.2.8 with previous version 0.2.6 dated 2017-08-15

Title: Species Distribution Modelling Predictor Datasets
Description: Terrestrial and marine predictors for species distribution modelling from multiple sources, including WorldClim <http://www.worldclim.org/>,, ENVIREM <http://envirem.github.io/>, Bio-ORACLE <http://bio-oracle.org/> and MARSPEC <http://www.marspec.org/>.
Author: Samuel Bosch [aut, cre], Lennert Tyberghein [ctb], Olivier De Clerck [ctb]
Maintainer: Samuel Bosch <mail@samuelbosch.com>

Diff between sdmpredictors versions 0.2.6 dated 2017-08-15 and 0.2.8 dated 2018-07-19

 DESCRIPTION                       |   10 
 LICENSE                           |    2 
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More information about sdmpredictors at CRAN
Permanent link

Package drake updated to version 5.3.0 with previous version 5.2.1 dated 2018-06-19

Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://ropensci.github.io/drake/> and the online manual <https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre], Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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More information about drake at CRAN
Permanent link

Package portes updated to version 3.0 with previous version 2.1-4 dated 2017-05-05

Title: Portmanteau Tests for Univariate and Multivariate Time. Series Models
Description: Simulate a univariate and multivariate data from seasonal and nonseasonal time series models. It implements the popular univariate and multivariate portmanteau test statistics based on the asymptotic distributions and the Monte Carlo significance tests.
Author: Esam Mahdi and A. Ian McLeod
Maintainer: Esam Mahdi <emahdi@iugaza.edu.ps>

Diff between portes versions 2.1-4 dated 2017-05-05 and 3.0 dated 2018-07-19

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Permanent link

Package ggthemes updated to version 4.0.0 with previous version 3.5.0 dated 2018-05-07

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

Diff between ggthemes versions 3.5.0 dated 2018-05-07 and 4.0.0 dated 2018-07-19

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 ggthemes-4.0.0/ggthemes/NAMESPACE                                         |   20 
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 ggthemes-4.0.0/ggthemes/R/banking.R                                       |    7 
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More information about ggthemes at CRAN
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Package shadow updated to version 0.5.5 with previous version 0.5.3 dated 2018-05-16

Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre], Evyatar Erell [ctb], Itai Kloog [ctb], Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between shadow versions 0.5.3 dated 2018-05-16 and 0.5.5 dated 2018-07-19

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 10 files changed, 110 insertions(+), 87 deletions(-)

More information about shadow at CRAN
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Package rwalkr updated to version 0.3.4 with previous version 0.3.3 dated 2018-03-19

Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian data in tidy data form.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>)
Maintainer: Earo Wang <earo.wang@gmail.com>

Diff between rwalkr versions 0.3.3 dated 2018-03-19 and 0.3.4 dated 2018-07-19

 DESCRIPTION           |   10 +++++-----
 MD5                   |    8 ++++----
 NEWS.md               |    4 ++++
 R/soda.R              |    2 +-
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 5 files changed, 14 insertions(+), 10 deletions(-)

More information about rwalkr at CRAN
Permanent link

New package disto with initial version 0.1.0
Package: disto
Type: Package
Title: Unified Interface to Distance, Dissimilarity, Similarity Matrices
Version: 0.1.0
Authors@R: person("KS", "Srikanth", email = "sri.teach@gmail.com", role = c("aut", "cre"))
Description: Provides a high level API to interface over sources storing distance, dissimilarity, similarity matrices with matrix style extraction, replacement and other utilities. Currently, in-memory dist object backend is supported.
URL: https://github.com/talegari/disto
BugReports: https://github.com/talegari/disto/issues
Imports: proxy (>= 0.4.19), dplyr (>= 0.7.4), assertthat (>= 0.2.0), fastmatch(>= 1.1.0), tidyr (>= 0.8.0), factoextra (>= 1.0.5), ggplot2 (>= 2.2.1), broom (>= 0.4.4), fastcluster (>= 1.1.25),
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.0.1
Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.4),
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-12 17:48:55 UTC; srikanth
Author: KS Srikanth [aut, cre]
Maintainer: KS Srikanth <sri.teach@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-19 10:20:06 UTC

More information about disto at CRAN
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New package bor with initial version 0.1.0
Package: bor
Type: Package
Title: Transforming Behavioral Observation Records into Data Matrices
Version: 0.1.0
Authors@R: c( person("David N", "Sousa", email = "davidnsousa@gmail.com", role = c("aut", "cre")), person("Joao R", "Daniel", email = "joaordaniel@gmail.com", role = "aut", comment = c(ORCID = "https://orcid.org/0000-0001-6609-2014")))
Description: Transforms focal observations' data, where different types of social interactions can be recorded by multiple observers, into asymmetric data matrices. Each cell in these matrices provides counts on the number of times a specific type of social interaction was initiated by the row subject and directed to the column subject.
Imports: stats (>= 3.4.2)
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-12 16:31:50 UTC; david
Author: David N Sousa [aut, cre], Joao R Daniel [aut] (<https://orcid.org/0000-0001-6609-2014>)
Maintainer: David N Sousa <davidnsousa@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-19 10:20:10 UTC

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New package baytrends with initial version 1.0.7
Package: baytrends
Type: Package
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized Additive Modeling (GAM) approach. The model development includes selecting a GAM structure to describe nonlinear seasonally-varying changes over time, incorporation of hydrologic variability via either a river flow or salinity, the use of an intervention to deal with method or laboratory changes suspected to impact data values, and representation of left- and interval-censored data. The approach has been applied to water quality data in the Chesapeake Bay, a major estuary on the east coast of the United States to provide insights to a range of management- and research-focused questions.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Version: 1.0.7
Date: 2018-07-12
Maintainer: Erik Leppo <Erik.Leppo@tetratech.com>
Depends: R (>= 3.2.0), lubridate, mgcv
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: devtools, fitdistrplus, imputeTS, knitr, nlme, pander, readxl, rmarkdown, testthat
Imports: XML, dataRetrieval, digest, gdata, memoise, methods, plyr, survival, zCompositions
URL: https://github.com/tetratech/baytrends
VignetteBuilder: knitr
Collate: 'a1_smwrQW_qw-class.R' 'a2_smwrQW_lcens-class.R' 'a3_smwrQW_mcens-class.R' 'analysisOrganizeData.R' 'appendDateFeatures.R' 'as.lcens.R' 'as.mcens.R' 'as.qw.R' 'baytrends.R' 'checkRange.R' 'chkParameter.R' 'closeOut.R' 'data.R' 'detrended.flow.R' 'detrended.salinity.R' 'expectMaxFunctions.r' 'findFile.R' 'flwAveragePred.R' 'fmtPval.R' 'gamDiff.R' 'gamPlotCalc.r' 'gamPlotDisp.R' 'gamTables.R' 'gamTest.r' 'getUSGSflow.R' 'headers2.R' 'imputeCensored.R' 'initializeResults.r' 'layerAggregation.R' 'loadData.R' 'loadExcel.R' 'mergeFlow.R' 'mergeSalinity.R' 'qw.export.R' 'qw.import.R' 'reAttDF.R' 'saveDF.R' 'seasAdjflow2.R' 'selectData.R' 'smwrBase_baseDay.R' 'smwrBase_baseDay2decimal.R' 'smwrBase_dectime.R' 'smwrBase_dectime2Date.R' 'smwrBase_eventProcessing.R' 'smwrBase_fillMissing.R' 'smwrBase_group2row.R' 'smwrBase_importRDB.R' 'smwrBase_isLike.R' 'smwrBase_na2miss.R' 'smwrBase_z%cn%.R' 'smwrGraphs_addCaption.R' 'smwrGraphs_colorPlot.R' 'smwrGraphs_datePretty.R' 'smwrGraphs_lineWt.R' 'smwrGraphs_linearPretty.R' 'smwrGraphs_month.USGS.R' 'smwrGraphs_namePretty.R' 'smwrGraphs_numericData.R' 'smwrGraphs_refLine.R' 'smwrGraphs_renderPretty.R' 'smwrGraphs_setColor.R' 'smwrGraphs_setExplan.R' 'smwrGraphs_setGD.R' 'smwrGraphs_setMargin.R' 'smwrGraphs_setMultiPlot.R' 'smwrGraphs_setPage.R' 'smwrGraphs_setPlot.R' 'smwrGraphs_strip.blanks.R' 'smwrGraphs_timePlot.R' 'smwrGraphs_timePretty.R' 'smwrGraphs_transData.R' 'smwrGraphs_xyPlot.R' 'smwrQW_censoring.R' 'smwrQW_is.na.R' 'smwrQW_mcenKM.R' 'smwrQW_mcenMLE.R' 'smwrQW_mcenROS.R' 'smwrQW_mdlMLE.R' 'smwrQW_mdlROS.R' 'smwrQW_pcodeNWISqw.R' 'smwrQW_x_Arith-censored.R' 'smwrQW_x_Math-censored.R' 'smwrQW_x_View.r' 'smwrQW_x_add.R' 'smwrQW_x_as.character.R' 'smwrQW_x_as.data.frame.R' 'smwrQW_x_as.double.R' 'smwrQW_x_c.R' 'smwrQW_x_censorlevels.R' 'smwrQW_x_censpp.R' 'smwrQW_x_convert2qw.R' 'smwrQW_x_convertFqw.R' 'smwrQW_x_dlimit.R' 'smwrQW_x_format.R' 'smwrQW_x_importNWISqw.R' 'smwrQW_x_importQW.R' 'smwrQW_x_imputeLessThans.R' 'smwrQW_x_length.R' 'smwrQW_x_makeColNames.R' 'smwrQW_x_mdlKM.R' 'smwrQW_x_mdlKMstats.R' 'smwrQW_x_mean.qw.R' 'smwrQW_x_meanStats.R' 'smwrQW_x_medianStats.R' 'smwrQW_x_print.censMCT.R' 'smwrQW_x_print.censQuantile.R' 'smwrQW_x_print.censReg.R' 'smwrQW_x_print.censStats.R' 'smwrQW_x_print.summary.censReg.R' 'smwrQW_x_printData.R' 'smwrQW_x_quantile.R' 'smwrQW_x_qw2mcens.R' 'smwrQW_x_qwCoalesce.R' 'smwrQW_x_ratio.R' 'smwrQW_x_rbindQW.R' 'smwrQW_x_readNWQLdl.R' 'smwrQW_x_residuals.censReg.R' 'smwrQW_x_sdlFill.R' 'smwrQW_x_show-censored.R' 'smwrQW_x_sort.censored.R' 'smwrQW_x_splitQual.R' 'smwrQW_x_str.R' 'smwrQW_x_subset.R' 'smwrQW_x_summary.R' 'smwrQW_x_summary.censReg.R' 'smwrQW_x_vcov.censReg.R' 'smwrQW_x_z%eq%.R' 'smwrStats_rmse.R' 'smwrStats_vif.R' 'supportFunctions.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2018-07-12 16:08:08 UTC; Erik.Leppo
Repository: CRAN
Date/Publication: 2018-07-19 10:20:13 UTC

More information about baytrends at CRAN
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Package rplos updated to version 0.8.2 with previous version 0.8.0 dated 2017-11-03

Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based search 'API' (<http://api.plos.org/>) provided by the Public Library of Science journals to search their articles. Functions are included for searching for articles, retrieving articles, making plots, doing 'faceted' searches, 'highlight' searches, and viewing results of 'highlighted' searches in a browser.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package groupedstats updated to version 0.0.2 with previous version 0.0.1 dated 2018-07-05

Title: Grouped Statistical Analyses in a Tidy Way
Description: Collection of functions to run statistical tests across all levels of multiple grouping variables.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package bomrang updated to version 0.2.2 with previous version 0.2.1 dated 2018-06-16

Title: Australian Government Bureau of Meteorology (BOM) Data from R
Description: Provides functions to interface with Australian Government Bureau of Meteorology (BOM) data, fetching data and returning a tidy data frame of précis forecasts, historical and current weather data from stations, agriculture bulletin data, BOM 0900 or 1500 weather bulletins or a raster stack object of satellite imagery from GeoTIFF files. Data (c) Australian Government Bureau of Meteorology Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See <http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>), Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>), Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>), Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>), James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>), Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package spacesRGB updated to version 1.1-1 with previous version 1.0-4 dated 2018-06-04

Title: Standard and User-Defined RGB Color Spaces, with Conversion Between RGB and CIE XYZ
Description: Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>

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Package mkin updated to version 0.9.47.2 with previous version 0.9.47.1 dated 2018-02-06

Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers and a choice of the optimisation methods made available by the 'FME' package. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using compiled C functions. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph] (<https://orcid.org/0000-0003-4371-6538>), Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>

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Package httpuv updated to version 1.4.5 with previous version 1.4.4.2 dated 2018-07-02

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>

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Package BE updated to version 0.1.1 with previous version 0.1.0 dated 2018-06-18

Title: Bioequivalence Study Data Analysis
Description: Analyze bioequivalence study data with industrial strength. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design. Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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New package ApacheLogProcessor with initial version 0.2.3
Package: ApacheLogProcessor
Type: Package
Title: Process the Apache Web Server Log Files
Version: 0.2.3
Date: 2018-07-18
Author: Diogo Silveira Mendonca
Maintainer: Diogo Silveira Mendonca <diogosmendonca@gmail.com>
Description: Provides capabilities to process Apache HTTPD Log files.The main functionalities are to extract data from access and error log files to data frames.
License: LGPL-3 | file LICENSE
URL: https://github.com/diogosmendonca/ApacheLogProcessor
BugReports: https://github.com/diogosmendonca/ApacheLogProcessor/issues
Imports: foreach, parallel, doParallel, utils, stringr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-19 02:09:54 UTC; 09513592740
Repository: CRAN
Date/Publication: 2018-07-19 07:30:08 UTC

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

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

2018-07-05 1.0.0

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

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

2018-07-05 0.1.0

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Package PRISMAstatement updated to version 1.0.2 with previous version 1.0.1 dated 2016-10-11

Title: Plot Flow Charts According to the "PRISMA" Statement
Description: Plot a PRISMA <http://prisma-statement.org/> flow chart describing the identification, screening, eligibility and inclusion or studies in systematic reviews. PRISMA is an evidence-based minimum set of items for reporting in systematic reviews and meta-analyses. PRISMA focuses on the reporting of reviews evaluating randomized trials, but can also be used as a basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>

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Wed, 18 Jul 2018

New package rzeit2 with initial version 0.1.0
Package: rzeit2
Type: Package
Title: Client for the ZEIT ONLINE Content API
Version: 0.1.0
Authors@R: person("Jan", "Dix", email = "jan.dix@uni-konstanz.de", role = c("aut", "cre"))
Description: Interface to gather newspaper articles from 'DIE ZEIT' and 'ZEIT ONLINE', based on a multilevel query <http://developer.zeit.de/>. A personal API key is required for usage.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.2.0)
BugReports: https://github.com/jandix/rzeit2/issues
LazyData: true
RoxygenNote: 6.0.1
Imports: anytime, ggplot2, httr, jsonlite, rvest, stringr, xml2
Suggests: dplyr, ggthemes, knitr, rmarkdown, robotstxt, tidytext
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-11 08:04:20 UTC; jan
Author: Jan Dix [aut, cre]
Maintainer: Jan Dix <jan.dix@uni-konstanz.de>
Repository: CRAN
Date/Publication: 2018-07-18 23:00:03 UTC

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Package microplot updated to version 1.0-41 with previous version 1.0-40 dated 2018-07-15

Title: Microplots (Sparklines) in 'LaTeX', 'Word', 'HTML', 'Excel'
Description: The microplot function writes a set of R graphics files to be used as microplots (sparklines) in tables in either 'LaTeX', 'HTML', 'Word', or 'Excel' files. For 'LaTeX', we provide methods for the Hmisc::latex() generic function to construct 'latex' tabular environments which include the graphs. These can be used directly with the operating system 'pdflatex' or 'latex' command, or by using one of 'Sweave', 'knitr', 'rmarkdown', or 'Emacs org-mode' as an intermediary. For 'MS Word', the msWord() function uses the 'flextable' package to construct 'Word' tables which include the graphs. There are several distinct approaches for constructing HTML files. The simplest is to use the msWord() function with argument filetype="html". Alternatively, use either 'Emacs org-mode' or the htmlTable::htmlTable() function to construct an 'HTML' file containing tables which include the graphs. See the documentation for our as.htmlimg() function. For 'Excel' use on 'Windows', the file examples/irisExcel.xls includes 'VBA' code which brings the individual panels into individual cells in the spreadsheet. Examples in the examples and demo subdirectories are shown with 'lattice' graphics, 'ggplot2' graphics, and 'base' graphics. Examples for 'LaTeX' include 'Sweave' (both 'LaTeX'-style and 'Noweb'-style), 'knitr', 'emacs org-mode', and 'rmarkdown' input files and their 'pdf' output files. Examples for 'HTML' include 'org-mode' and 'Rmd' input files and their webarchive 'HTML' output files. In addition, the as.orgtable() function can display a data.frame in an 'org-mode' document. The examples for 'MS Word' (with either filetype="docx" or filetype="html") work with all operating systems. The package does not require the installation of 'LaTeX' or 'MS Word' to be able to write '.tex' or '.docx' files.
Author: Richard M. Heiberger, with contributions from Karen Byron and Nooreen Dabbish.
Maintainer: Richard M. Heiberger <rmh@temple.edu>

Diff between microplot versions 1.0-40 dated 2018-07-15 and 1.0-41 dated 2018-07-18

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Package LS2Wstat updated to version 2.1-1 with previous version 2.1 dated 2018-05-21

Title: A Multiscale Test of Spatial Stationarity for LS2W Processes
Description: Wavelet-based methods for testing stationarity and quadtree segmenting of images, see Taylor et al (2014) <doi:10.1080/00401706.2013.823890>.
Author: Sarah Taylor [aut], Matt Nunes [aut, cre], Idris Eckley [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between LS2Wstat versions 2.1 dated 2018-05-21 and 2.1-1 dated 2018-07-18

 DESCRIPTION             |   14 +++++++-------
 MD5                     |    4 ++--
 man/LS2Wstat-package.Rd |    2 +-
 3 files changed, 10 insertions(+), 10 deletions(-)

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New package IntNMF with initial version 1.2.0
Package: IntNMF
Type: Package
Title: Integrative Clustering of Multiple Genomic Dataset
Version: 1.2.0
Date: 2018-07-17
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Prabhakar Chalise <pchalise@kumc.edu>
Description: Carries out integrative clustering analysis using multiple types of genomic dataset using integrative Non-negative Matrix factorization.
License: GPL-2
Depends: R (>= 3.5), MASS, NMF, mclust, cluster, InterSIM
NeedsCompilation: no
Packaged: 2018-07-18 15:39:55 UTC; pchalise
Repository: CRAN
Date/Publication: 2018-07-18 22:40:19 UTC
RoxygenNote: 6.0.1

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New package binman with initial version 0.1.1
Package: binman
Title: A Binary Download Manager
Version: 0.1.1
Authors@R: c( person("John", "Harrison", , "johndharrison0@gmail.com", role = "aut", comment = "original author"), person("Ju Yeong", "Kim", , "jkim2345@fredhutch.org", role = "cre", comment = "rOpenSci maintainer"))
Description: Tools and functions for managing the download of binary files. Binary repositories are defined in 'YAML' format. Defining new pre-download, download and post-download templates allow additional repositories to be added.
Depends: R (>= 3.3)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr, knitr, rmarkdown
Imports: rappdirs, yaml, httr, jsonlite, xml2, utils, stats, assertthat, semver
URL: https://github.com/ropensci/binman
URLNote: https://github.com/ropensci/binman
BugReports: https://github.com/ropensci/binman/issues
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-17 23:07:40 UTC; jkim
Author: John Harrison [aut] (original author), Ju Yeong Kim [cre] (rOpenSci maintainer)
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>
Repository: CRAN
Date/Publication: 2018-07-18 22:40:08 UTC

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Package binhf updated to version 1.0-3 with previous version 1.0-2 dated 2018-06-07

Title: Haar-Fisz Functions for Binomial Data
Description: Binomial Haar-Fisz transforms for Gaussianization as in Nunes and Nason (2009).
Author: Matt Nunes <nunesrpackages@gmail.com>
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between binhf versions 1.0-2 dated 2018-06-07 and 1.0-3 dated 2018-07-18

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Package robotstxt updated to version 0.6.2 with previous version 0.6.0 dated 2018-02-11

Title: A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker
Description: Provides functions to download and parse 'robots.txt' files. Ultimately the package makes it easy to check if bots (spiders, crawler, scrapers, ...) are allowed to access specific resources on a domain.
Author: Peter Meissner [aut, cre], Oliver Keys [ctb], Rich Fitz John [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>

Diff between robotstxt versions 0.6.0 dated 2018-02-11 and 0.6.2 dated 2018-07-18

 DESCRIPTION                   |   14 +-
 MD5                           |   14 +-
 NEWS.md                       |   16 ++
 R/get_robotstxt.R             |    2 
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Package maditr updated to version 0.5.2 with previous version 0.5.1 dated 2018-05-10

Title: Pipe-Style Interface for 'data.table'
Description: Package provides pipe-style interface for 'data.table'. It preserves all 'data.table' features without significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data manipulation tasks. For example, you can write 'mtcars %>% take(mean(mpg), by = am)' for aggregation or 'mtcars %>% let(hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional aggregation/modification. 'query_if' function translates its arguments one-to-one to '[.data.table' method. Additionally there are some conveniences such as automatic 'data.frame' conversion to 'data.table'.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>

Diff between maditr versions 0.5.1 dated 2018-05-10 and 0.5.2 dated 2018-07-18

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Package future.batchtools updated to version 0.7.1 with previous version 0.7.0 dated 2018-05-06

Title: A Future API for Parallel and Distributed Processing using 'batchtools'
Description: Implementation of the Future API on top of the 'batchtools' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, not only on your local machine or ad-hoc cluster of machines, but also via high-performance compute ('HPC') job schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS', e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future.batchtools versions 0.7.0 dated 2018-05-06 and 0.7.1 dated 2018-07-18

 DESCRIPTION                    |    8 -
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 NAMESPACE                      |    5 
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 27 files changed, 381 insertions(+), 314 deletions(-)

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Package NlinTS updated to version 1.3.3 with previous version 1.3.2 dated 2018-03-16

Title: Non Linear Time Series Analysis
Description: Models for time series forecasting and causality detection. The main functionalities of this package consist of a neural network Vector Auto-Regressive model, the classical Granger causality test C.W.J.Granger (1980) <doi:10.1016/0165-1889(80)90069-X>, and a non-linear version of it based on feedforward neural networks.
Author: Youssef Hmamouche [aut, cre], Sylvain Barthelemy [cph]
Maintainer: Youssef Hmamouche <hmamoucheyussef@gmail.com>

Diff between NlinTS versions 1.3.2 dated 2018-03-16 and 1.3.3 dated 2018-07-18

 DESCRIPTION                      |    8 ++++----
 MD5                              |   28 ++++++++++++++--------------
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 inst/include/Tests.h             |    4 ++--
 src/CDynamicCausality.cpp        |    2 +-
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 15 files changed, 58 insertions(+), 57 deletions(-)

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Package nanotime updated to version 0.2.2 with previous version 0.2.1 dated 2018-07-01

Title: Nanosecond-Resolution Time for R
Description: Full 64-bit resolution date and time support with resolution up to nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between nanotime versions 0.2.1 dated 2018-07-01 and 0.2.2 dated 2018-07-18

 ChangeLog                 |    7 +++++++
 DESCRIPTION               |    8 ++++----
 MD5                       |    8 ++++----
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 5 files changed, 26 insertions(+), 11 deletions(-)

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Package perccalc updated to version 1.0.2 with previous version 1.0.1 dated 2018-03-30

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

Diff between perccalc versions 1.0.1 dated 2018-03-30 and 1.0.2 dated 2018-07-18

 DESCRIPTION                           |    7 
 MD5                                   |   15 
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 9 files changed, 1067 insertions(+), 645 deletions(-)

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Package foreign updated to version 0.8-70.2 with previous version 0.8-70.1 dated 2018-07-13

Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>

Diff between foreign versions 0.8-70.1 dated 2018-07-13 and 0.8-70.2 dated 2018-07-18

 ChangeLog       |    5 +++--
 DESCRIPTION     |    8 ++++----
 MD5             |    8 ++++----
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 5 files changed, 16 insertions(+), 14 deletions(-)

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New package TaxicabCA with initial version 0.1.0
Package: TaxicabCA
Type: Package
Title: Taxicab Correspondence Analysis
Version: 0.1.0
Suggests: GA, testthat
Imports: grDevices, graphics, stats, utils
Author: Jacques Allard and Vartan Choulakian
Maintainer: Jacques Allard <jacques.allard@gmail.com>
Description: Computation and visualization of Taxicab Correspondence Analysis, Choulakian (2006) <doi:10.1007/s11336-004-1231-4>. Classical correspondence analysis (CA) is a statistical method to analyse 2-dimensional tables of positive numbers and is typically applied to contingency tables (Benzecri, J.-P. (1973). L'Analyse des Donnees. Volume II. L'Analyse des Correspondances. Paris, France: Dunod). Classical CA is based on the Euclidean distance. Taxicab CA is like classical CA but is based on the Taxicab or Manhattan distance. For some tables, Taxicab CA gives more informative results than classical CA.
License: GPL (>= 2)
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-12 14:53:20 UTC; Jacques
Repository: CRAN
Date/Publication: 2018-07-18 15:20:03 UTC

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New package TangPoemR with initial version 0.1.0
Package: TangPoemR
Type: Package
Title: Write Chinese Tang Poems
Version: 0.1.0
Author: Yanni Li, Yongyuan Liang
Maintainer: Yongyuan Liang <charlotte9762@hotmail.com>
Description: Write Chinese Tang Poems automatically.
Imports: jiebaR
License: GPL (>= 2)
Depends: R (>= 3.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-11 11:01:22 UTC; LYN
Repository: CRAN
Date/Publication: 2018-07-18 13:10:13 UTC

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New package RPS with initial version 1.0.0
Package: RPS
Type: Package
Title: Resistant Procrustes Superimposition
Version: 1.0.0
Authors@R: c(person("Guillermo Andres", "Pacheco", email = "guillermopacheco.exa@gmail.com", role = c("aut", "cre")), person("Sebastian", "Torcida", email = "unisebas@gmail.com", role = "aut"), person("Viviana", "Ferragine", email = "viviana.ferraggine@gmail.com", role = "aut"), person("Federico", "Lotto", email = "federicolotto@gmail.com@gmail.com", role = "aut"))
Maintainer: Guillermo Andres Pacheco <guillermopacheco.exa@gmail.com>
Description: Based on RPS tools, a rather complete resistant shape analysis of 2D and 3D datasets based on landmarks can be performed. In addition, landmark-based resistant shape analysis of individual asymmetry in 2D for matching or object symmetric structures is also possible.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: geomorph, MASS, igraph, ape, matlab, Gmedian
NeedsCompilation: no
Packaged: 2018-07-12 00:27:36 UTC; Guillermo
Author: Guillermo Andres Pacheco [aut, cre], Sebastian Torcida [aut], Viviana Ferragine [aut], Federico Lotto [aut]
Repository: CRAN
Date/Publication: 2018-07-18 13:50:03 UTC

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Package rmpw updated to version 0.0.4 with previous version 0.0.3 dated 2018-01-04

Title: Causal Mediation Analysis Using Weighting Approach
Description: We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity analysis strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998617749561>.
Author: Xu Qin, Guanglei Hong, and Fan Yang
Maintainer: Xu Qin <xuqin@uchicago.edu>

Diff between rmpw versions 0.0.3 dated 2018-01-04 and 0.0.4 dated 2018-07-18

 DESCRIPTION       |    8 +--
 MD5               |   10 ++--
 NAMESPACE         |    1 
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Package revengc updated to version 1.0.2 with previous version 1.0.1 dated 2018-07-17

Title: Reverse Engineering Decoupled and Censored Data
Description: An issue occurs when authors do not reveal clear information. Decoupled variables (e.g. separate averages) and numeric censoring (e.g. between ages 10-15) are reoccurring instances found in areas ranging from demographic and epidemiological data to ecological inference problems. Decoupled variables provide no availability for cross tabulations while censoring obscures the true underlying values. The revengc R package was developed to reverse engineer this unclear information that is continually reported by many well-established organizations (e.g. World Health Organization (WHO), Centers for Disease Control and Prevention (CDC), World Bank, and various national censuses). There are two main functions in revengc and both fit data to a Poisson or Quasi-Poisson distribution. The estimated_lambda function takes a univariate censored frequency table and approximates its lambda (average) value. The rec function calculates an uncensored bivariate table from decoupled and summarized arguments.
Author: Samantha Duchscherer [aut, cre], UT-Battelle, LLC [cph]
Maintainer: Samantha Duchscherer <sam.duchscherer@gmail.com>

Diff between revengc versions 1.0.1 dated 2018-07-17 and 1.0.2 dated 2018-07-18

 DESCRIPTION                             |    8 ++++----
 MD5                                     |   10 +++++-----
 README.md                               |    2 +-
 inst/doc/duchscherer-stewart-urban.ltx  |    2 +-
 inst/doc/duchscherer-stewart-urban.pdf  |binary
 vignettes/duchscherer-stewart-urban.ltx |    2 +-
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New package r4lineups with initial version 0.1.1
Package: r4lineups
Title: Statistical Inference on Lineup Fairness
Version: 0.1.1
Authors@R: c( person("Colin", "Tredoux", email = "colin.tredoux@uct.ac.za", role = c("aut", "cre")), person("Tamsyn", "Naylor", email = "tmnaylor@outlook.com", role = "aut"))
Maintainer: Colin Tredoux <colin.tredoux@uct.ac.za>
Description: Since the early 1970s eyewitness testimony researchers have recognised the importance of estimating properties such as lineup bias (is the lineup biased against the suspect, leading to a rate of choosing higher than one would expect by chance?), and lineup size (how many reasonable choices are in fact available to the witness? A lineup is supposed to consist of a suspect and a number of additional members, or foils, whom a poor-quality witness might mistake for the perpetrator). Lineup measures are descriptive, in the first instance, but since the earliest articles in the literature researchers have recognised the importance of reasoning inferentially about them. This package contains functions to compute various properties of laboratory or police lineups, and is intended for use by researchers in forensic psychology and/or eyewitness testimony research. Among others, the r4lineups package includes functions for calculating lineup proportion, functional size, various estimates of effective size, diagnosticity ratio, homogeneity of the diagnosticity ratio, ROC curves for confidence x accuracy data and the degree of similarity of faces in a lineup.
Depends: R (>= 3.4.0)
Imports: boot, dplyr, ggplot2, ggrepel, here, magick, magrittr, pROC, psych, purrr, stats, utils
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: knitr, rmarkdown, pander
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-12 07:42:53 UTC; Tamsyn Naylor
Author: Colin Tredoux [aut, cre], Tamsyn Naylor [aut]
Repository: CRAN
Date/Publication: 2018-07-18 13:20:02 UTC

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New package evian with initial version 2.0.0
Package: evian
Type: Package
Title: Evidential Analysis of Genetic Association Data
Version: 2.0.0
Depends: R (>= 3.2.5), ProfileLikelihood, sandwich, foreach, doParallel
Author: Dr. Lisa J Strug <lisa.strug@utoronto.ca>; Dr. Zeynep Baskurt <zeynep.baskurt@sickkids.ca>; Bowei Xiao <bowei.xiao@sickkids.ca>; Ted Chiang <theodorechiang@gmail.com>
Maintainer: Bowei Xiao <bowei.xiao@sickkids.ca>
Description: Evidential regression analysis for dichotomous and quantitative outcome data. The following references described the methods in this package: Strug, L. J., Hodge, S. E., Chiang, T., Pal, D. K., Corey, P. N., & Rohde, C. (2010) <doi:10.1038/ejhg.2010.47>. Strug, L. J., & Hodge, S. E. (2006) <doi:10.1159/000094709>. Royall, R. (1997) <ISBN:0-412-04411-0>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-11 16:22:17 UTC; bowei
Repository: CRAN
Date/Publication: 2018-07-18 13:10:06 UTC

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Package dynutils updated to version 1.0.0 with previous version 0.1.0 dated 2018-06-24

Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://github.com/dynverse/dynverse>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

Diff between dynutils versions 0.1.0 dated 2018-06-24 and 1.0.0 dated 2018-07-18

 dynutils-0.1.0/dynutils/R/run_until_exit.R                        |only
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 dynutils-0.1.0/dynutils/tests/testthat/test-run_until_exit.R      |only
 dynutils-1.0.0/dynutils/DESCRIPTION                               |   23 +-
 dynutils-1.0.0/dynutils/MD5                                       |   82 +++++-----
 dynutils-1.0.0/dynutils/NAMESPACE                                 |   20 ++
 dynutils-1.0.0/dynutils/R/RcppExports.R                           |   28 +++
 dynutils-1.0.0/dynutils/R/add_class.R                             |    4 
 dynutils-1.0.0/dynutils/R/check_packages.R                        |only
 dynutils-1.0.0/dynutils/R/expand_matrix.R                         |    4 
 dynutils-1.0.0/dynutils/R/extend_with.R                           |   11 +
 dynutils-1.0.0/dynutils/R/inherit_default_params.R                |   16 -
 dynutils-1.0.0/dynutils/R/install_packages.R                      |   54 +++---
 dynutils-1.0.0/dynutils/R/mapdf.R                                 |only
 dynutils-1.0.0/dynutils/R/package.R                               |   59 ++++++-
 dynutils-1.0.0/dynutils/R/pritt.R                                 |    4 
 dynutils-1.0.0/dynutils/R/random_time_string.R                    |    3 
 dynutils-1.0.0/dynutils/R/scaling.R                               |    8 
 dynutils-1.0.0/dynutils/R/tibble.R                                |   58 ++++++-
 dynutils-1.0.0/dynutils/README.md                                 |   16 -
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 dynutils-1.0.0/dynutils/inst                                      |only
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 dynutils-1.0.0/dynutils/man/scale_quantile.Rd                     |    4 
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 dynutils-1.0.0/dynutils/tests/testthat/test-check_packages.R      |only
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 dynutils-1.0.0/dynutils/tests/testthat/test-tibble.R              |   45 ++++-
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 48 files changed, 529 insertions(+), 185 deletions(-)

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New package CliftLRD with initial version 0.1-1
Package: CliftLRD
Type: Package
Title: Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent for Irregularly Sampled Time Series
Version: 0.1-1
Date: 2018-07-09
Author: Matt Nunes [aut, cre], Marina Knight [aut]
Authors@R: c(person("Matt", "Nunes", role=c("aut","cre"),email="nunesrpackages@gmail.com"), person("Marina", "Knight", role="aut"))
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Description: Implementation of Hurst exponent estimators based on complex-valued lifting wavelet energy from Knight, M. I and Nunes, M. A. (2018) <doi:10.1007/s11222-018-9820-8>.
License: GPL-2
Depends: CNLTreg, liftLRD
Suggests: fracdiff
NeedsCompilation: no
Packaged: 2018-07-12 09:14:38 UTC; nunes
Repository: CRAN
Date/Publication: 2018-07-18 14:00:03 UTC

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Package CASMAP updated to version 0.6.0 with previous version 0.5.9 dated 2018-07-05

Title: Detection of Statistically Significant Combinations of SNPs in Association Mapping
Description: A significant pattern mining-based toolbox for region-based genome-wide association studies and higher-order epistasis analyses, implementing the methods described in Llinares-López et al. (2017) <doi:10.1093/bioinformatics/btx071>.
Author: Felipe Llinares-López [aut, cph], Laetitia Papaxanthos [aut, cph], Damian Roqueiro [aut, cph], Matthew Baker [ctr], Mikołaj Rybiński [ctr], Uwe Schmitt [ctr], Dean Bodenham [aut, cre, cph], Karsten Borgwardt [aut, fnd, cph]
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>

Diff between CASMAP versions 0.5.9 dated 2018-07-05 and 0.6.0 dated 2018-07-18

 DESCRIPTION                                |    6 +++---
 MD5                                        |    8 ++++----
 inst/include/Summary.h                     |    3 ++-
 src/SignificantFeaturesSearchTaroneCmh.cpp |    3 ++-
 src/pval.cpp                               |   10 ++++++++--
 5 files changed, 19 insertions(+), 11 deletions(-)

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Package VCA updated to version 1.3.4 with previous version 1.3.3 dated 2017-07-12

Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.
Author: Andre Schuetzenmeister [aut, cre], Florian Dufey [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>

Diff between VCA versions 1.3.3 dated 2017-07-12 and 1.3.4 dated 2018-07-18

 DESCRIPTION                   |    8 
 MD5                           |   21 -
 NAMESPACE                     |    1 
 R/plot.R                      |  565 ++++++++++++++++++++++++++++++++++--------
 R/vca.R                       |  132 ++++-----
 inst/ChangeLog.txt            |   12 
 inst/UnitTests/runit.remlMM.R |   11 
 man/VCA-Package.Rd            |    4 
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 12 files changed, 674 insertions(+), 263 deletions(-)

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New package thor with initial version 1.0.1
Package: thor
Title: Interface to 'LMDB'
Version: 1.0.1
Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"), email = "rich.fitzjohn@gmail.com"), person("Howard", "Chu", role = "cph"), person("Symas Corporation", role = "cph"), person("Martin", "Hedenfalk", role = "cph"), person("The OpenLDAP Foundation", role = "cph"))
Description: Key-value store, implemented as a wrapper around 'LMDB'; the "lightning memory-mapped database" <https://symas.com/lmdb/>. 'LMDB' is a transactional key value store that uses a memory map for efficient access. This package wraps the entire 'LMDB' interface, providing objects for transactions and cursors.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/richfitz/thor
BugReports: https://github.com/richfitz/thor/issues
Imports: R6, storr
Suggests: ids, knitr, rmarkdown, testthat
RoxygenNote: 6.0.1
VignetteBuilder: knitr
ByteCompile: true
Encoding: UTF-8
Language: en-GB
NeedsCompilation: yes
Packaged: 2018-07-11 07:55:21 UTC; rich
Author: Rich FitzJohn [aut, cre], Howard Chu [cph], Symas Corporation [cph], Martin Hedenfalk [cph], The OpenLDAP Foundation [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-18 13:00:03 UTC

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Package SmoothWin updated to version 2.0.0 with previous version 1.0.0 dated 2017-09-06

Title: Soft Windowing on Linear Regression
Description: The main function in the package utilizes a windowing function in the form of an exponential weighting function to linear models. The bandwidth and sharpness of the window are controlled by two parameters. Then, a series of tests are used to identify the right parameters of the window (see Charles Kervrann (2004) <doi:10.1007/978-3-540-24672-5_11>).
Author: Hamed Haselimashhadi <hamedhm@ebi.ac.uk>
Maintainer: Hamed Haselimashhadi <hamedhm@ebi.ac.uk>

Diff between SmoothWin versions 1.0.0 dated 2017-09-06 and 2.0.0 dated 2018-07-18

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New package r511 with initial version 0.1.1
Package: r511
Type: Package
Title: Work with the Bay Area Transportation Commission Application Programming Interface
Version: 0.1.1
Author: Tom Buckley
Maintainer: Tom Buckley <tom@tbuckl.com>
Description: For the 9 counties in the San Francisco Bay area the Metropolitan Transportation Commission maintains an Application Programming Interface with information on more than 20 transit operators. This package allows users to retrieve information about transit schedules in the General Transit Feed Specification as published by the Metropolitan Transportation Commission at the following url: <https://511.org/developers/list/apis/>.
License: GPL
Encoding: UTF-8
LazyData: true
Imports: dplyr, tibble, httr, xml2, assertthat
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-11 01:43:39 UTC; tbuck
Repository: CRAN
Date/Publication: 2018-07-18 12:10:02 UTC

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Package liftLRD updated to version 1.0-8 with previous version 1.0-7 dated 2018-05-22

Title: Wavelet Lifting Estimators of the Hurst Exponent for Regularly and Irregularly Sampled Time Series
Description: Implementations of Hurst exponent estimators based on the relationship between wavelet lifting scales and wavelet energy of Knight et al (2017) <doi:10.1007/s11222-016-9698-2>.
Author: Marina Knight [aut], Guy Nason [ctb], Matt Nunes [aut, cre]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between liftLRD versions 1.0-7 dated 2018-05-22 and 1.0-8 dated 2018-07-18

 DESCRIPTION            |   14 +++++++-------
 MD5                    |    4 ++--
 man/liftLRD-package.Rd |    2 +-
 3 files changed, 10 insertions(+), 10 deletions(-)

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Package CNLTtsa updated to version 0.1-2 with previous version 0.1 dated 2017-03-08

Title: Complex-Valued Wavelet Lifting for Univariate and Bivariate Time Series Analysis
Description: Implementations of recent complex-valued wavelet spectral procedures for analysis of irregularly sampled signals, see Hamilton et al (2018) <doi:10.1080/00401706.2017.1281846>.
Author: Jean Hamilton [aut], Matt Nunes [aut, cre], Marina Knight [ctb], Piotr Fryzlewicz [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between CNLTtsa versions 0.1 dated 2017-03-08 and 0.1-2 dated 2018-07-18

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 build/partial.rdb        |binary
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 15 files changed, 48 insertions(+), 45 deletions(-)

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Package CNLTreg updated to version 0.1-2 with previous version 0.1 dated 2017-03-04

Title: Complex-Valued Wavelet Lifting for Signal Denoising
Description: Implementations of recent complex-valued wavelet shrinkage procedures for smoothing irregularly sampled signals, see Hamilton et al (2018) <doi:10.1080/00401706.2017.1281846>.
Author: Matt Nunes [aut, cre], Marina Knight [aut], Jean Hamilton [ctb], Piotr Fryzlewicz [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between CNLTreg versions 0.1 dated 2017-03-04 and 0.1-2 dated 2018-07-18

 DESCRIPTION            |   19 +++++++++++--------
 MD5                    |   22 +++++++++++-----------
 R/denoisepermCh.R      |    2 +-
 R/fwtnppermC.R         |    2 +-
 build/partial.rdb      |binary
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New package adpss with initial version 0.1.0
Package: adpss
Title: Design and Analysis of Locally or Globally Efficient Adaptive Designs
Version: 0.1.0
Authors@R: person("Kosuke", "Kashiwabara", email = "kashiwabara-tky@umin.ac.jp", role = c("aut", "cre"))
Description: Provides the functions for planning and conducting a clinical trial with adaptive sample size determination. Maximal statistical efficiency will be exploited even when dramatic or multiple adaptations are made. Such a trial consists of adaptive determination of sample size at an interim analysis and implementation of frequentist statistical test at the interim and final analysis with a prefixed significance level. The required assumptions for the stage-wise test statistics are independent and stationary increments and normality. Predetermination of adaptation rule is not required.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
URL: https://github.com/ca4wa/R-adpss
LinkingTo: Rcpp (>= 0.12.17)
Imports: Rcpp (>= 0.12.17)
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-11 07:40:56 UTC; Epistat
Author: Kosuke Kashiwabara [aut, cre]
Maintainer: Kosuke Kashiwabara <kashiwabara-tky@umin.ac.jp>
Repository: CRAN
Date/Publication: 2018-07-18 13:00:07 UTC

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New package tmvmixnorm with initial version 1.0.1
Package: tmvmixnorm
Type: Package
Title: Efficient Sampling Truncated Scale of Normals with Constraints
Version: 1.0.1
Authors@R: c(person("Ting Fung (Ralph)", "Ma", email = "tingfung.ma@wisc.edu", role = c("cre", "aut")), person("Sujit K.", "Ghosh", email = "sujit_ghosh@ncsu.edu", role = "aut"), person("Yifang", "Li", role = "aut"))
Maintainer: Ting Fung (Ralph) Ma <tingfung.ma@wisc.edu>
Description: Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong. Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributed random numbers. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multivariate Student-t distribution is also developed. Moreover, the proposed method and computation remain valid for high dimensional and strong dependence scenarios. Empirical results in Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> illustrated the superior performance in terms of various criteria (e.g. mixing and integrated auto-correlation time).
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2.0)
Imports: stats
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-10 21:08:16 UTC; Ralph
Author: Ting Fung (Ralph) Ma [cre, aut], Sujit K. Ghosh [aut], Yifang Li [aut]
Repository: CRAN
Date/Publication: 2018-07-18 11:30:02 UTC

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New package tatest with initial version 1.0
Package: tatest
Type: Package
Title: Two-Group Ta-Test
Version: 1.0
Date: 2018-07-10
Author: Yuan-De Tan
Maintainer: Yuan-De Tan <tanyuande@gmail.com>
Description: The ta-test is a modified two-sample or two-group t-test of Gosset (1908). In small samples with less than 15 replicates,the ta-test significantly reduces type I error rate but has almost the same power with the t-test and hence can greatly enhance reliability or reproducibility of discoveries in biology and medicine. The ta-test can test single null hypothesis or multiple null hypotheses without needing to correct p-values.
License: GPL-3
Depends: R (>= 3.3.0), stats, base,utils
LazyLoad: yes
NeedsCompilation: no
Packaged: 2018-07-10 19:34:46 UTC; yuandet
Repository: CRAN
Date/Publication: 2018-07-18 11:30:05 UTC

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New package rhli with initial version 0.0.1
Package: rhli
Title: FIS 'MarketMap C-Toolkit'
Version: 0.0.1
Authors@R: c( person("Kevin", "Keane", email = "krkeane@qoma.io", role = c("aut", "cre")), person("Qoma", "LLC", email = "info@qoma.io", role = "cph"))
Description: Complete access from 'R' to the FIS 'MarketMap C-Toolkit' ('FAME C-HLI'). 'FAME' is a fully integrated software and database management system from FIS that provides the following capabilities: Time series and cross-sectional data management; Financial calculation, data analysis, econometrics, and forecasting; Table generation and detailed multicolor, presentation-quality report writing; Multicolor, presentation-quality graphics; "What-if" analysis; Application development and structured programming; Data transfer to and from other applications; Tools for building customized graphical user interfaces.
Depends: R (>= 3.0)
License: AGPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: methods
Suggests: testthat
URL: https://github.com/qomaio/rhli
BugReports: https://github.com/qomaio/rhli/issues
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2018-07-11 00:29:09 UTC; Kevin R. Keane
Author: Kevin Keane [aut, cre], Qoma LLC [cph]
Maintainer: Kevin Keane <krkeane@qoma.io>
Repository: CRAN
Date/Publication: 2018-07-18 11:40:03 UTC

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Package nngeo updated to version 0.2.0 with previous version 0.1.8 dated 2018-05-15

Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C implementation of the Vincenty Formula for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers.
Author: Michael Dorman [aut, cre], Johnathan Rush [ctb], Ian Hough [ctb], Jan Antala [ctb, cph] (Author of C code for Vincenty distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between nngeo versions 0.1.8 dated 2018-05-15 and 0.2.0 dated 2018-07-18

 DESCRIPTION                      |   15 +++-
 LICENSE                          |    2 
 MD5                              |   23 ++++---
 NEWS.md                          |   10 ++-
 R/st_connect.R                   |  126 ++++++++++++++++++++++-----------------
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 14 files changed, 120 insertions(+), 91 deletions(-)

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