Sat, 15 Oct 2016

Package tint updated to version 0.0.3 with previous version 0.0.2 dated 2016-10-07

Title: Tint is not Tufte
Description: A 'tufte'-alike style for 'rmarkdown'.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between tint versions 0.0.2 dated 2016-10-07 and 0.0.3 dated 2016-10-15

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New package eulerr with initial version 0.1.0
Package: eulerr
Title: Area-Proportional Euler Diagrams
Version: 0.1.0
Authors@R: person("Johan", "Larsson", email = "johanlarsson@outlook.com", role = c("aut", "cre"))
Description: If possible, generates exactly area-proportional Euler diagrams, or otherwise approximately proportional diagrams using numeric optimization. A Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented.
Depends: R (>= 3.3.1)
Imports: assertthat (>= 0.1), randtoolbox (>= 1.17), grDevices, utils, stats, graphics
Suggests: knitr, rmarkdown, testthat, venneuler
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/jolars/eulerr
BugReports: https://github.com/jolars/eulerr/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-15 22:34:30 UTC; johan
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Repository: CRAN
Date/Publication: 2016-10-16 02:45:21

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Package sunburstR updated to version 0.6.3 with previous version 0.6.2 dated 2016-09-19

Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org), Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib, https://gist.github.com/kerryrodden/7090426), Kent Russell [aut, cre] (R interface), Florian Breitwieser [ctb] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between sunburstR versions 0.6.2 dated 2016-09-19 and 0.6.3 dated 2016-10-15

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Package SSN updated to version 1.1.8 with previous version 1.1.7 dated 2016-03-17

Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>

Diff between SSN versions 1.1.7 dated 2016-03-17 and 1.1.8 dated 2016-10-15

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Package SimReg updated to version 3.0 with previous version 2.1 dated 2016-08-16

Title: Similarity Regression
Description: Functions for performing Bayesian similarity regression, and evaluating the probability of association between sets of ontological terms and binary response vector. A random model is compared with one in which the log odds of a true response is linked to the semantic similarity between terms and a latent characteristic ontological profile.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>

Diff between SimReg versions 2.1 dated 2016-08-16 and 3.0 dated 2016-10-15

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Package rredlist updated to version 0.2.0 with previous version 0.1.0 dated 2016-01-26

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]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rredlist versions 0.1.0 dated 2016-01-26 and 0.2.0 dated 2016-10-15

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New package nucim with initial version 0.5.3
Package: nucim
Title: Nucleus Imaging Toolbox
Version: 0.5.3
Date: 2016-10-14
Author: Volker Schmid
Maintainer: Volker Schmid <stats@volkerschmid.de>
Depends: R (>= 3.0.0)
biocViews:
Imports: bioimagetools, EBImage, fields
Suggests: parallel
Description: Code for analysis of microscopy images of nuclei.
License: GPL-3
URL: http://volkerschmid.de
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-14 14:39:36 UTC; schmid
Repository: CRAN
Date/Publication: 2016-10-15 18:52:12

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Package npbr updated to version 1.4 with previous version 1.3 dated 2016-06-20

Title: Nonparametric Boundary Regression
Description: A variety of functions for the best known and most innovative approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smoothed, unrestricted as well as constrained fits under both separate and multiple shape constraints. They cover robust approaches to outliers as well as data envelopment techniques based on piecewise polynomials, splines, local linear fitting, extreme values and kernel smoothing. The package also seamlessly allows for Monte Carlo comparisons among these different estimation methods. Its use is illustrated via a number of empirical applications and simulated examples.
Author: Abdelaati Daouia <Abdelaati.Daouia@tse-fr.eu>, Thibault Laurent <thibault.laurent@univ-tlse1.fr>, Hohsuk Noh <word5810@gmail.com>
Maintainer: Thibault Laurent <thibault.laurent@univ-tlse1.fr>

Diff between npbr versions 1.3 dated 2016-06-20 and 1.4 dated 2016-10-15

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Package multiwave updated to version 1.1 with previous version 1.0 dated 2015-10-28

Title: Estimation of Multivariate Long-Memory Models Parameters
Description: Computation of an estimation of the long-memory parameters and the long-run covariance matrix using a multivariate model (Lobato (1999) <10.1016/S0304-4076(98)00038-4>; Shimotsu (2007) <10.1016/j.jeconom.2006.01.003>). Two semi-parametric methods are implemented: a Fourier based approach (Shimotsu (2007) <10.1016/j.jeconom.2006.01.003>) and a wavelet based approach (Achard and Gannaz (2016) <10.1111/jtsa.12170>).
Author: Sophie Achard [aut, cre], Irene Gannaz [aut]
Maintainer: Sophie Achard <sophie.achard@gipsa-lab.fr>

Diff between multiwave versions 1.0 dated 2015-10-28 and 1.1 dated 2016-10-15

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Package metasens updated to version 0.3-1 with previous version 0.3-0 dated 2016-02-17

Title: Advanced Statistical Methods to Model and Adjust for Bias in Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 "Small-Study Effects in Meta-Analysis": - Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>; - limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>; - upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>.
Author: Guido Schwarzer [aut, cre], James Carpenter [aut], Gerta Rücker [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between metasens versions 0.3-0 dated 2016-02-17 and 0.3-1 dated 2016-10-15

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Package inlmisc updated to version 0.2.1 with previous version 0.1.2 dated 2016-09-16

Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics, performing raster-based analysis, processing MODFLOW-based models, and overlaying multi-polygon objects. Used to support packages and scripts written by researchers at the United States Geological Survey (USGS) Idaho National Laboratory (INL) Project Office.
Author: Jason Fisher [aut, cre]
Maintainer: Jason Fisher <jfisher@usgs.gov>

Diff between inlmisc versions 0.1.2 dated 2016-09-16 and 0.2.1 dated 2016-10-15

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Package Grace updated to version 0.4.3 with previous version 0.4.2 dated 2016-10-04

Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <sen-zhao@sen-zhao.com>

Diff between Grace versions 0.4.2 dated 2016-10-04 and 0.4.3 dated 2016-10-15

 DESCRIPTION       |    9 ++++-----
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New package gpg with initial version 0.2
Package: gpg
Type: Package
Title: GNU Privacy Guard for R
Version: 0.2
Authors@R: person("Jeroen", "Ooms", email = "jeroen.ooms@stat.ucla.edu", role = c("aut", "cre"))
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. Includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Note that some functionality depends on the version of GnuPG that is installed on the system. In particular GnuPG 2 mandates the use of 'gpg-agent' for entering passphrases, which only works if R runs in a terminal session.
License: MIT + file LICENSE
SystemRequirements: GPGME: libgpgme11-dev (deb), gpgme-devel (rpm) gpgme (brew)
RoxygenNote: 5.0.1.9000
Imports: curl
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-10-14 14:24:08 UTC; jeroen
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Repository: CRAN
Date/Publication: 2016-10-15 18:52:00

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Package dynsurv updated to version 0.3-3 with previous version 0.3-2 dated 2016-08-30

Title: Dynamic Models for Survival Data
Description: Functions to fit time-varying coefficient models for interval censored and right censored survival data. Three major approaches are implemented: 1) Bayesian Cox model with time-independent, time-varying or dynamic coefficients for right censored and interval censored data; 2) Spline based time-varying coefficient Cox model for right censored data; 3) Transformation model with time-varying coefficients for right censored data using estimating equations.
Author: Wenjie Wang [cre, aut], Ming-Hui Chen [aut], Xiaojing Wang [aut], Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>

Diff between dynsurv versions 0.3-2 dated 2016-08-30 and 0.3-3 dated 2016-10-15

 ChangeLog              |   11 
 DESCRIPTION            |   21 -
 MD5                    |   26 -
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 man/bcos.Rd            |    2 
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 src/DynamicCoxModel.h  |   17 
 src/DynamicGORHModel.h |   19 -
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 src/IntRegModel.h      |    2 
 src/TimeIndepModel.h   |    4 
 src/TimeVaryingModel.h |   12 
 14 files changed, 700 insertions(+), 671 deletions(-)

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Package CollocInfer updated to version 1.0.3 with previous version 1.0.2 dated 2015-08-20

Title: Collocation Inference for Dynamic Systems
Description: These functions implement collocation-inference for continuous-time and discrete-time stochastic processes. They provide model-based smoothing, gradient-matching, generalized profiling and forwards prediction error methods.
Author: Giles Hooker <gjh27@cornell.edu>, Luo Xiao <lx42@cornell.edu>, James Ramsay <ramsay@psych.mcgill.ca>
Maintainer: Giles Hooker <gjh27@cornell.edu>

Diff between CollocInfer versions 1.0.2 dated 2015-08-20 and 1.0.3 dated 2016-10-15

 DESCRIPTION             |    8 ++++----
 MD5                     |    6 +++---
 R/CollocInferPlots.R    |   11 ++++++-----
 man/CollocInferPlots.rd |    4 +++-
 4 files changed, 16 insertions(+), 13 deletions(-)

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New package types with initial version 1.0.0
Package: types
Title: Type Annotations
Version: 1.0.0
Authors@R: person("Jim", "Hester", email = "james.f.hester@gmail.com", role = c("aut", "cre"))
Description: Provides a simple type annotation for R that is usable in scripts, in the R console and in packages. It is intended as a convention to allow other packages to use the type information to provide error checking, automatic documentation or optimizations.
Depends: R (>= 3.0.3)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2016-10-14 14:55:50 UTC; jhester
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Repository: CRAN
Date/Publication: 2016-10-15 11:31:52

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New package RSarules with initial version 1.0
Package: RSarules
Type: Package
Title: Random Sampling Association Rules from a Transaction Dataset
Version: 1.0
Date: 2016-10-11
Author: Xiaoying Sun, Guoqi Qian and Yuehua Wu
Maintainer: Xiaoying Sun <sunying@mathstat.yorku.ca>
Depends: R (>= 3.3.1), arules (>= 1.4.1), Matrix (>= 1.2.6)
Imports: methods, stats
Suggests: MultiOrd
Description: Implements the Gibbs sampling algorithm to randomly sample association rules with one pre-chosen item as the consequent from a transaction dataset. The Gibbs sampling algorithm was proposed in G. Qian, C.R. Rao, X. Sun and Y. Wu (2016) <DOI:10.1073/pnas.1604553113>.
License: GPL-3
Repository: CRAN
NeedsCompilation: no
Packaged: 2016-10-14 14:25:07 UTC; Michelle
Date/Publication: 2016-10-15 11:21:10

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New package RAC with initial version 1.0.1
Package: RAC
Version: 1.0.1
Date: 2016-09-29
Title: R Package for Aqua Culture
Authors@R: c(person("Baldan", "D.", role = c("aut", "cre"), email = "damiano.baldan91@gmail.com"), person("Palazzo", "D.", role = "ctb"), person("Porporato", "E.M.D", role = "ctb"), person("Brigolin", "D.", role = "ctb"))
Maintainer: Baldan D. <damiano.baldan91@gmail.com>
Depends: R (>= 3.1.0), matrixStats, rstudioapi, plotrix
Suggests: MASS, knitr, rmarkdown
Description: Solves the bioenergetic balance for different aquaculture sea fish (Sea Bream and Sea Bass) and shellfish (Mussel and Clam) both at individual and population scale.
License: MIT + file LICENSE
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-10-14 14:22:01 UTC; Damiano
Author: Baldan D. [aut, cre], Palazzo D. [ctb], Porporato E.M.D [ctb], Brigolin D. [ctb]
Repository: CRAN
Date/Publication: 2016-10-15 11:16:27

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Package mnormt updated to version 1.5-5 with previous version 1.5-4 dated 2016-03-08

Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

Diff between mnormt versions 1.5-4 dated 2016-03-08 and 1.5-5 dated 2016-10-15

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 mnormt-1.5-5/mnormt/R/mnormt.R    |    4 +---
 mnormt-1.5-5/mnormt/inst/CITATION |    2 +-
 mnormt-1.5-5/mnormt/man/dmnorm.Rd |   35 +++++++++++++++++++++--------------
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 8 files changed, 52 insertions(+), 52 deletions(-)

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New package fontLiberation with initial version 0.1.0
Package: fontLiberation
Title: Liberation Fonts
Version: 0.1.0
Authors@R: c( person("Lionel", "Henry", , "lionel@rstudio.com", "cre"), person("Pravin Satpute", role = "aut"), person("Steve Matteson", role = "aut"), person("Red Hat, Inc", role = "cph"), person("Google Corporation", role = "cph"))
Description: A placeholder for the Liberation fontset intended for the `fontquiver` package. This fontset covers the 12 combinations of families (sans, serif, mono) and faces (plain, bold, italic, bold italic) supported in R graphics devices.
Depends: R (>= 3.0)
License: file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-14 14:21:59 UTC; lionel
Author: Lionel Henry [cre], Pravin Satpute [aut], Steve Matteson [aut], Red Hat, Inc [cph], Google Corporation [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Repository: CRAN
Date/Publication: 2016-10-15 11:24:17

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Package BEACH updated to version 1.1.2 with previous version 1.1.1 dated 2016-10-05

Title: Biometric Exploratory Analysis Creation House
Description: A platform is provided for interactive analyses with a goal of totally easy to develop, deploy, interact, and explore (TEDDIE). Using this package, users can create customized analyses and make them available to end users who can perform interactive analyses and save analyses to RTF or HTML files. It allows developers to focus on R code for analysis, instead of dealing with html or shiny code.
Author: Danni Yu [aut, cre], Michael Man [aut], ChenChen Yu [com]
Maintainer: Danni Yu <danni.yu@gmail.com>

Diff between BEACH versions 1.1.1 dated 2016-10-05 and 1.1.2 dated 2016-10-15

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 9 files changed, 111 insertions(+), 61 deletions(-)

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Package ADPclust updated to version 0.7 with previous version 0.6.5 dated 2015-12-03

Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast Clustering Using Adaptive Density Peak Detection). The work is built and improved upon the idea of Rodriguez and Laio (2014)<DOI:10.1126/science.1242072>. ADPclust clusters data by finding density peaks in a density-distance plot generated from local multivariate Gaussian density estimation. It includes an automatic centroids selection and parameter optimization algorithm, which finds the number of clusters and cluster centroids by comparing average silhouettes on a grid of testing clustering results; It also includes a user interactive algorithm that allows the user to manually selects cluster centroids from a two dimensional "density-distance plot". Here is the research article associated with this package: "Wang, Xiao-Feng, and Yifan Xu (2015)<DOI:10.1177/0962280215609948> Fast clustering using adaptive density peak detection." Statistical methods in medical research". url: http://smm.sagepub.com/content/early/2015/10/15/0962280215609948.abstract.
Author: Yifan (Ethan) Xu [aut, cre], Xiao-Feng Wang [aut]
Maintainer: Yifan (Ethan) Xu <ethan.yifanxu@gmail.com>

Diff between ADPclust versions 0.6.5 dated 2015-12-03 and 0.7 dated 2016-10-15

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 63 files changed, 547 insertions(+), 439 deletions(-)

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