Sat, 07 Mar 2015

Package TimeWarp updated to version 1.0.11 with previous version 1.0-7 dated 2013-04-03

Title: Date Calculations and Manipulation
Description: Date sequence, relative date calculations, and date manipulation with business days and holidays. Works with Date and POSIXt classes.
Author: Tony Plate, Jeffrey Horner, Lars Hansen
Maintainer: Tony Plate

Diff between TimeWarp versions 1.0-7 dated 2013-04-03 and 1.0.11 dated 2015-03-07

 TimeWarp-1.0-7/TimeWarp/TODO.txt                 |only
 TimeWarp-1.0-7/TimeWarp/portingNotes.txt         |only
 TimeWarp-1.0.11/TimeWarp/DESCRIPTION             |   15 -
 TimeWarp-1.0.11/TimeWarp/MD5                     |   46 ++--
 TimeWarp-1.0.11/TimeWarp/NEWS                    |   12 +
 TimeWarp-1.0.11/TimeWarp/R/dateMatch.R           |  240 +++++++++++------------
 TimeWarp-1.0.11/TimeWarp/R/dateParse.R           |   70 ++++++
 TimeWarp-1.0.11/TimeWarp/R/dateSeq.R             |   37 +--
 TimeWarp-1.0.11/TimeWarp/R/dateWarp.R            |  135 ++++--------
 TimeWarp-1.0.11/TimeWarp/R/holidays.R            |   16 -
 TimeWarp-1.0.11/TimeWarp/R/misc.R                |    2 
 TimeWarp-1.0.11/TimeWarp/inst                    |only
 TimeWarp-1.0.11/TimeWarp/man/TimeWarp-package.Rd |    3 
 TimeWarp-1.0.11/TimeWarp/man/dateAlign.Rd        |   19 -
 TimeWarp-1.0.11/TimeWarp/man/dateMatch.Rd        |    3 
 TimeWarp-1.0.11/TimeWarp/man/dateParse.Rd        |   12 -
 TimeWarp-1.0.11/TimeWarp/man/dateSeq.Rd          |    5 
 TimeWarp-1.0.11/TimeWarp/man/holidays.Rd         |    3 
 TimeWarp-1.0.11/TimeWarp/man/pitfalls.Rd         |   35 +++
 TimeWarp-1.0.11/TimeWarp/tests/dateMatch.Rt      |    5 
 TimeWarp-1.0.11/TimeWarp/tests/dateParse.Rt      |    2 
 TimeWarp-1.0.11/TimeWarp/tests/dateSeq.Rt        |   80 +++++++
 TimeWarp-1.0.11/TimeWarp/tests/dateShift.Rt      |    2 
 TimeWarp-1.0.11/TimeWarp/tests/dateWarp.Rt       |    5 
 TimeWarp-1.0.11/TimeWarp/tests/holidays.Rt       |   11 -
 25 files changed, 463 insertions(+), 295 deletions(-)

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New package SID with initial version 1.0
Package: SID
Type: Package
Title: Structural Intervention Distance
Version: 1.0
Date: 2015-03-07
Author: Jonas Peters
Encoding: UTF-8
Imports: pcalg, igraph, RBGL, Matrix
Maintainer: Jonas Peters
Description: The code computes the structural intervention distance (SID) between a true directed acyclic graph (DAG) and an estimated DAG. Definition and details about the implementation can be found in J. Peters and P. Bühlmann: "Structural intervention distance (SID) for evaluating causal graphs", Neural Computation 27, pages 771-799, 2015.
License: FreeBSD
Packaged: 2015-03-07 14:35:03 UTC; jopeters
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-07 17:35:02

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Package openxlsx updated to version 2.4.0 with previous version 2.2.1 dated 2014-10-18

Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre], Luca Braglia [ctb]
Maintainer: Alexander Walker

Diff between openxlsx versions 2.2.1 dated 2014-10-18 and 2.4.0 dated 2015-03-07

 DESCRIPTION                  |   12 
 MD5                          |  153 +++--
 NAMESPACE                    |    8 
 NEWS                         |   43 +
 R/RcppExports.R              |   48 +
 R/StyleClass.R               |  133 ++++-
 R/WorkbookClass.R            |  921 ++++++++++++++++++++++++++++-------
 R/baseXML.R                  |   81 ++-
 R/borderFunctions.R          |  267 +++++-----
 R/helperFunctions.R          |  151 +++--
 R/loadWorkbook.R             |  484 +++++++++++++-----
 R/openxlsxCoerce.R           |only
 R/readWorkbook.R             |  533 ++++++++++++++++++--
 R/wrappers.R                 |  789 ++++++++++++++++++++++--------
 R/writeData.R                |  174 ------
 R/writeDataTable.R           |   28 -
 R/writexlsx.R                |   76 ++
 build/vignette.rds           |binary
 inst/doc/Introduction.Rnw    |  102 ++-
 inst/doc/Introduction.pdf    |binary
 inst/doc/formatting.Rnw      |   85 +--
 inst/doc/formatting.pdf      |binary
 inst/loadExample.xlsx        |binary
 inst/readTest.xlsx           |binary
 man/addFilter.Rd             |    7 
 man/addStyle.Rd              |   10 
 man/addWorksheet.Rd          |    7 
 man/conditionalFormat.Rd     |   25 
 man/conditionalFormatting.Rd |only
 man/convertFromExcelRef.Rd   |    3 
 man/convertToDate.Rd         |   14 
 man/convertToDateTime.Rd     |   10 
 man/createStyle.Rd           |   13 
 man/createWorkbook.Rd        |    3 
 man/deleteData.Rd            |    9 
 man/freezePane.Rd            |    7 
 man/getBaseFont.Rd           |    3 
 man/getCellRefs.Rd           |    3 
 man/getDateOrigin.Rd         |only
 man/getStyles.Rd             |    7 
 man/insertImage.Rd           |    3 
 man/insertPlot.Rd            |   11 
 man/loadWorkbook.Rd          |   16 
 man/mergeCells.Rd            |    3 
 man/modifyBaseFont.Rd        |    3 
 man/names.Rd                 |    3 
 man/openXL.Rd                |    3 
 man/openxlsx.Rd              |    3 
 man/pageSetup.Rd             |    7 
 man/read.xlsx.Rd             |   54 +-
 man/readWorkbook.Rd          |   23 
 man/removeCellMerge.Rd       |    3 
 man/removeColWidths.Rd       |    9 
 man/removeFilter.Rd          |    3 
 man/removeRowHeights.Rd      |    5 
 man/removeWorksheet.Rd       |    5 
 man/renameWorksheet.Rd       |    3 
 man/replaceStyle.Rd          |    7 
 man/saveWorkbook.Rd          |    5 
 man/setColWidths.Rd          |    7 
 man/setFooter.Rd             |    5 
 man/setHeader.Rd             |    7 
 man/setHeaderFooter.Rd       |    3 
 man/setRowHeights.Rd         |    3 
 man/sheets.Rd                |    3 
 man/showGridLines.Rd         |    9 
 man/worksheetOrder.Rd        |    3 
 man/write.xlsx.Rd            |    9 
 man/writeData.Rd             |   15 
 man/writeDataTable.Rd        |   17 
 src/RcppExports.cpp          |  181 +++++--
 src/cppFunctions.cpp         | 1101 +++++++++++++++++++++++++++++--------------
 tests                        |only
 vignettes/Introduction.Rnw   |  102 ++-
 vignettes/formatting.Rnw     |   85 +--
 75 files changed, 4154 insertions(+), 1774 deletions(-)

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Package tm.plugin.lexisnexis updated to version 1.2 with previous version 1.1 dated 2014-06-11

Title: Import Articles from LexisNexis Using the tm Text Mining Framework
Description: Provides a tm Source to create corpora from articles exported from the LexisNexis content provider as HTML files. It is able to read both text content and meta-data information (including source, date, title, author and pages).
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat

Diff between tm.plugin.lexisnexis versions 1.1 dated 2014-06-11 and 1.2 dated 2015-03-07

 tm.plugin.lexisnexis-1.1/tm.plugin.lexisnexis/inst/texts/lexisnexis_test.html     |only
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/DESCRIPTION                         |   14 -
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/MD5                                 |   14 -
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/NEWS                                |    3 
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/R/readLexisNexisHTML.R              |   92 ++++++----
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/inst/texts/lexisnexis_test_en.html  |only
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/inst/texts/lexisnexis_test_fr.html  |only
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/man/LexisNexisSource.Rd             |    4 
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/man/tm.plugin.lexisnexis-package.Rd |    2 
 tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/tests                               |only
 10 files changed, 83 insertions(+), 46 deletions(-)

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Package SimSeq updated to version 1.3.0 with previous version 1.2.0 dated 2014-12-10

Title: Nonparametric Simulation of RNA-Seq Data
Description: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.
Author: Samuel Benidt
Maintainer: Samuel Benidt

Diff between SimSeq versions 1.2.0 dated 2014-12-10 and 1.3.0 dated 2015-03-07

 DESCRIPTION           |    8 ++++----
 MD5                   |   15 ++++++++-------
 NEWS                  |    6 ++++++
 R/SimData.R           |    7 +++++--
 data/kidney.rda       |binary
 inst                  |only
 man/SimData.Rd        |    9 ++++++---
 man/SimSeq-package.Rd |    4 ++--
 man/kidney.Rd         |   18 +++++++++++++++---
 9 files changed, 46 insertions(+), 21 deletions(-)

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Package RcppParallel updated to version 4.3.4 with previous version 4.3.3 dated 2014-10-21

Title: Parallel Programming Tools for Rcpp
Description: High level functions for doing 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, cre], Romain Francois [aut, cph], 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: JJ Allaire

Diff between RcppParallel versions 4.3.3 dated 2014-10-21 and 4.3.4 dated 2015-03-07

 RcppParallel-4.3.3/RcppParallel/src/Makevars.win               |only
 RcppParallel-4.3.4/RcppParallel/DESCRIPTION                    |   37 ++++-
 RcppParallel-4.3.4/RcppParallel/MD5                            |   42 ++++--
 RcppParallel-4.3.4/RcppParallel/NAMESPACE                      |    1 
 RcppParallel-4.3.4/RcppParallel/NEWS                           |    7 -
 RcppParallel-4.3.4/RcppParallel/R/build.R                      |only
 RcppParallel-4.3.4/RcppParallel/R/hooks.R                      |only
 RcppParallel-4.3.4/RcppParallel/R/options.R                    |   35 -----
 RcppParallel-4.3.4/RcppParallel/README.md                      |   48 -------
 RcppParallel-4.3.4/RcppParallel/inst/include/RcppParallel.h    |   13 +
 RcppParallel-4.3.4/RcppParallel/inst/presentations             |only
 RcppParallel-4.3.4/RcppParallel/man/RcppParallel-package.Rd    |   18 ++
 RcppParallel-4.3.4/RcppParallel/man/RcppParallelLibs.Rd        |only
 RcppParallel-4.3.4/RcppParallel/man/setThreadOptions.Rd        |    4 
 RcppParallel-4.3.4/RcppParallel/src/Makevars                   |   66 +++++++---
 RcppParallel-4.3.4/RcppParallel/src/options.cpp                |    4 
 RcppParallel-4.3.4/RcppParallel/src/tbb/build/common_rules.inc |    6 
 RcppParallel-4.3.4/RcppParallel/src/tbb/build/windows.inc      |   25 ++-
 RcppParallel-4.3.4/RcppParallel/tests                          |only
 19 files changed, 171 insertions(+), 135 deletions(-)

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