Sun, 13 Nov 2016

Package RxODE updated to version 0.5-5 with previous version 0.5-1 dated 2015-10-21

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual.
Author: Melissa Hallow [aut], Wenping Wang [aut, cre]
Maintainer: Wenping Wang <wwang8198@gmail.com>

Diff between RxODE versions 0.5-1 dated 2015-10-21 and 0.5-5 dated 2016-11-13

 DESCRIPTION                                          |   22 
 MD5                                                  |  655 +++---
 NAMESPACE                                            |   34 
 R/RxODE.R                                            |  737 +++---
 R/eventTable.R                                       |  366 +--
 R/genShinyApp.template.R                             |  403 +--
 demo/00Index                                         |    2 
 demo/demo1.R                                         |  116 -
 inst/Changes.txt                                     |  178 -
 inst/Install-windows.Rmd                             |  166 -
 inst/Porting                                         |   56 
 inst/THANKS                                          |   36 
 inst/TODO.txt                                        |   96 
 inst/common/call_dvode.c                             |    6 
 inst/doc/RxODE-intro.Rmd                             |  371 +--
 inst/doc/RxODE-intro.html                            |  692 ++----
 inst/doc/RxODE-syntax.Rmd                            |  295 +-
 inst/doc/RxODE-syntax.html                           |  540 ++---
 inst/doc/index.html                                  |only
 inst/driver_parsetree_no_inp.c                       |only
 inst/pkpd.g                                          |only
 inst/tran.c                                          |only
 inst/tran.g                                          |  124 -
 man/RxODE.Rd                                         |  582 ++---
 man/eventTable.Rd                                    |  286 +-
 man/genShinyApp.template.Rd                          |  148 -
 man/rx.initCmpMgr.Rd                                 |  160 -
 src/Makefile                                         |    4 
 src/Makefile.win                                     |   52 
 src/dparser/4calc.g                                  |   60 
 src/dparser/4calc.in                                 |    4 
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 src/dparser/COPYRIGHT                                |   18 
 src/dparser/D_BUILD_VERSION                          |    2 
 src/dparser/Makefile.new                             |only
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 src/dparser/make_dparser.1                           |  234 +-
 src/dparser/make_dparser.cat                         |  228 +-
 src/dparser/manual.html                              | 1638 +++++++--------
 src/dparser/my.g                                     |   12 
 src/dparser/orig-Makefile                            |  440 ++--
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 src/install.libs.R                                   |   62 
 src/ode/Makefile                                     |    4 
 src/ode/dlsoda.f                                     |   56 
 src/ode/opkda1_abbr.f                                |  229 +-
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 tests/Examples/RxODE.Rout.save                       |  116 -
 tests/Examples/eventTable.Rout.save                  |   66 
 tests/test-basic.R                                   |   48 
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 tests/test-parsing.R                                 |  200 -
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More information about RxODE at CRAN
Permanent link

Package RefManageR updated to version 0.13.1 with previous version 0.13.0 dated 2016-11-10

Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>

Diff between RefManageR versions 0.13.0 dated 2016-11-10 and 0.13.1 dated 2016-11-13

 DESCRIPTION             |    8 ++++----
 MD5                     |   10 +++++-----
 NAMESPACE               |    3 ++-
 R/04InternalFunctions.R |    4 ++--
 R/format.R              |    2 +-
 inst/doc/manual.pdf     |binary
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Package QuantTools updated to version 0.5.1 with previous version 0.5.0 dated 2016-10-13

Title: Enhanced Quantitative Trading Modelling
Description: Download and organize historical market data from multiple sources like Yahoo (<https://finance.yahoo.com>), Google (<https://www.google.com/ finance>), Finam (<https://www.finam.ru/profile/moex-akcii/sberbank/export/>) and IQFeed (<https://www.iqfeed.net/symbolguide/index.cfm?symbolguide=lookup>). Code your trading algorithms in modern C++11 with powerful event driven tick processing API including trading costs and exchange communication latency and transform detailed data seamlessly into R. In just few lines of code you will be able to visualize every step of your trading model from tick data to multi dimensional heat maps.
Author: Stanislav Kovalevsky
Maintainer: Stanislav Kovalevsky <so.kovalevsky@gmail.com>

Diff between QuantTools versions 0.5.0 dated 2016-10-13 and 0.5.1 dated 2016-11-13

 DESCRIPTION                       |   18 
 MD5                               |   24 
 NAMESPACE                         |    3 
 R/get_market_data.R               |  686 +++++++++---------
 R/iqfeed.R                        |  479 +++++++++----
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 man/get_market_data.Rd            |    6 
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 man/plot_ts.Rd                    |    2 
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Permanent link

New package PhyInformR with initial version 1.0
Package: PhyInformR
Type: Package
Title: Rapid Calculation of Phylogenetic Information Content
Version: 1.0
Date: 2016-10-29
Authors@R: c(person("Alex", "Dornburg",email="alex.dornburg@naturalsciences.org",role=c("aut","cre", "cph")),person("J. Nick", "Fisk", email="jnf3769@rit.edu",role=c("aut", "cph")),person("Jules", "Tamagnan",email="jules.tamagnan@yale.edu",role=c("aut", "cph")), person("Jeffrey","Townsend",email="jeffrey.townsend@yale.edu",role=c("aut", "cph")))
Maintainer: Alex Dornburg <alex.dornburg@naturalsciences.org>
Description: Enables rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory. These advances include modifications that incorporate uneven branch lengths and any model of nucleotide substitution to provide assessments of the phylogenetic utility of any given dataset or dataset partition. Also provides new tools for data visualization and routines optimized for rapid statistical calculations, including approaches making use of Bayesian posterior distributions and parallel processing. Users can apply these approaches toward screening datasets for phylogenetic/genomic information content.
License: GPL-3
Depends: R (>= 3.3.0)
Encoding: UTF-8
LazyData: true
Imports: phytools, splines, gplots, RColorBrewer, foreach, iterators, geiger, doParallel, gridExtra, hexbin, PBSmodelling, ape, ggplot2
NeedsCompilation: no
Packaged: 2016-11-13 19:09:16 UTC; admadornburg
Author: Alex Dornburg [aut, cre, cph], J. Nick Fisk [aut, cph], Jules Tamagnan [aut, cph], Jeffrey Townsend [aut, cph]
Repository: CRAN
Date/Publication: 2016-11-13 23:13:37

More information about PhyInformR at CRAN
Permanent link

Package peacots updated to version 1.3 with previous version 1.2 dated 2015-06-13

Title: Periodogram Peaks in Correlated Time Series
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

Diff between peacots versions 1.2 dated 2015-06-13 and 1.3 dated 2016-11-13

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New package ffstream with initial version 0.1.2
Package: ffstream
Title: Forgetting Factor Methods for Change Detection in Streaming Data
Version: 0.1.2
Author: Dean Bodenham
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>
Description: An implementation of the adaptive forgetting factor scheme described in Bodenham and Adams (2016) <doi:10.1007/s11222-016-9684-8> which adaptively estimates the mean and variance of a stream in order to detect multiple changepoints in streaming data. The implementation is in C++ and uses Rcpp. Additionally, implementations of the fixed forgetting factor scheme from the same paper, as well as the classic CUSUM and EWMA methods, are included.
Depends: R (>= 3.3.0)
License: GPL-2 | GPL-3
LazyData: true
LinkingTo: Rcpp
Imports: methods, Rcpp
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-11-13 15:59:08 UTC; dean
Repository: CRAN
Date/Publication: 2016-11-13 23:00:03

More information about ffstream at CRAN
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Package eDMA updated to version 1.2 with previous version 1.1 dated 2016-11-12

Title: Dynamic Model Averaging with Grid Search
Description: Perform Dynamic Model Averaging with grid search as in Dangl and Halling (2012) <doi:10.1016/j.jfineco.2012.06.005> using parallel computing.
Author: Leopoldo Catania & Nima Nonejad
Maintainer: Leopoldo Catania <leopoldo.catania@uniroma2.it>

Diff between eDMA versions 1.1 dated 2016-11-12 and 1.2 dated 2016-11-13

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Package edeaR updated to version 0.4.7 with previous version 0.4.4 dated 2016-09-21

Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Functions for exploratory and descriptive analysis of event based data. Can be used to import and export Xes-files, the IEEE eXtensible Event Stream standard (see <http://standards.ieee.org/findstds/standard/1849-2016.html> for more info). Provides methods for describing and selecting process data, and for preparing event log data for process mining.
Author: Gert Janssenswillen
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>

Diff between edeaR versions 0.4.4 dated 2016-09-21 and 0.4.7 dated 2016-11-13

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New package SmartSVA with initial version 0.1.0
Package: SmartSVA
Type: Package
Title: Implementation of Smart SVA
Version: 0.1.0
Author: Jun Chen <Chen.Jun2@mayo.edu>, Ehsan Behnam <behnamgh@usc.edu>
Maintainer: Jun Chen <Chen.Jun2@mayo.edu>
Description: Introduces an improved Surrogate Variable Analysis algorithm that automatically captures salient features from data in the presence of confounding factors. The algorithm is based on the popular 'SVA' package and proposes a revision on it that achieves 10 times faster running time while trading no accuracy loss in return.
License: GPL-3
Depends: sva, isva
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-11-11 21:41:04 UTC; Ehsan
Repository: CRAN
Date/Publication: 2016-11-13 16:57:27

More information about SmartSVA at CRAN
Permanent link

Package sjmisc updated to version 2.1.0 with previous version 2.0.1 dated 2016-10-31

Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/ or who are new to R), supporting following common tasks when working with data : 1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc. 2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package pkgKitten updated to version 0.1.4 with previous version 0.1.3 dated 2015-06-13

Title: Create Simple Packages Which Do not Upset R Package Checks
Description: Provides a function kitten() which creates cute little packages which pass R package checks. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between pkgKitten versions 0.1.3 dated 2015-06-13 and 0.1.4 dated 2016-11-13

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Package QCAGUI updated to version 2.5 with previous version 2.4 dated 2016-07-07

Title: Qualitative Comparative Analysis GUI
Description: This is an obsolete version of the package QCAGUI, which is now merged with package QCA.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between QCAGUI versions 2.4 dated 2016-07-07 and 2.5 dated 2016-11-13

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Package tesseract updated to version 1.2 with previous version 1.1 dated 2016-11-10

Title: Open Source OCR Engine
Description: An OCR engine with unicode (UTF-8) support that can recognize over 100 languages out of the box.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between tesseract versions 1.1 dated 2016-11-10 and 1.2 dated 2016-11-13

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Package Sim.DiffProc updated to version 3.6 with previous version 3.5 dated 2016-11-10

Title: Simulation of Diffusion Processes
Description: Provides the functions for simulating and modeling of stochastic differential equations (SDE's). Statistical analysis and simulation of the solution of SDE's enabled many searchers in different domains to use these equations to modeling practical problems, in financial and actuarial modeling and other areas of application. For example, modeling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996).
Author: Arsalane Chouaib Guidoum [cre, aut], Kamal Boukhetala [aut]
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>

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Package REBayes updated to version 0.73 with previous version 0.68 dated 2016-10-19

Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models and some other density estimation and regression methods based on convex optimization.
Author: Roger Koenker [aut, cre], Jiaying Gu [ctb], Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>

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More information about REBayes at CRAN
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Package GGally updated to version 1.3.0 with previous version 1.2.0 dated 2016-07-01

Title: Extension to 'ggplot2'
Description: The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs, ggduo, ggnostic, ggts, ggfacet, and ggally_*. Contributor for all functions.), Jason Crowley [aut] (ggparcoord), Di Cook [aut, ths] (ggscatmat, gglyph), Heike Hofmann [ths], Hadley Wickham [ths], Francois Briatte [aut] (ggcorr, ggnet, ggnet2), Moritz Marbach [aut] (ggnet, ggnet2), Edwin Thoen [aut] (ggsurv), Amos Elberg [aut] (ggnetworkmap), Joseph Larmarange [aut] (ggcoef)
Maintainer: Barret Schloerke <schloerke@gmail.com>

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More information about GGally at CRAN
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