Package DoE.base updated to version 0.27 with previous version 0.26-3 dated 2014-09-29

Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE Packages
Description: Package \pkg{DoE.base} creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class \code{design}, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre], Boyko Amarov [ctb], Hongquan Xu [ctb]
Maintainer: Ulrike Groemping

Diff between DoE.base versions 0.26-3 dated 2014-09-29 and 0.27 dated 2015-03-28

 DESCRIPTION                     |   14 +++----
 MD5                             |   68 +++++++++++++++++++-------------------
 NAMESPACE                       |    5 ++
 R/DesignAccessors.r             |   27 +++++++++++++--
 R/GRind.R                       |   19 ++++++++--
 R/fac.design.R                  |   71 +++++++++++++++++++++++++++++++---------
 R/fastlengths.R                 |   10 +++--
 R/halfnormal.R                  |   57 +++++++++++++++++++-------------
 R/length2.R                     |    6 ---
 R/lengths.R                     |only
 R/oa.design.R                   |   13 ++++++-
 R/planor2design.r               |    2 +
 R/plot.design.R                 |   23 +++++++++++-
 R/printandsummary.design.R      |    4 +-
 R/rerandomize.R                 |   52 +++++++++++++++++++++++++++--
 R/show.oas.R                    |   28 ++++++++++++---
 R/sysdata.rda                   |binary
 R/utilities.R                   |   59 +++++++++++++++++++++++++++++++++
 inst/NEWS                       |   62 +++++++++++++++++++++++++++++++++-
 man/GWLP.Rd                     |    8 ++--
 man/VSGFS.Rd                    |only
 man/class-design.Rd             |    8 +++-
 man/fac.design.Rd               |   15 ++++++--
 man/generalized.word.length.Rd  |   50 +++++++++++++++++-----------
 man/getblock.Rd                 |   16 +++++++--
 man/halfnormal.Rd               |   47 ++++++++++++++++----------
 man/oa.design.Rd                |    8 +++-
 man/oacat.Rd                    |   22 ++++++++++--
 man/planor2design.Rd            |    4 +-
 man/plot.design.Rd              |   13 +++----
 man/show.oas.Rd                 |   50 ++++++++++++++++++++++------
 tests/test_aggregate.Rout.save  |   12 ++++--
 tests/test_colorder.Rout.save   |   12 ++++--
 tests/test_cross.Rout.save      |   12 ++++--
 tests/test_qua.design.Rout.save |   15 +++++---
 tests/test_reshape.Rout.save    |   15 +++++---
 36 files changed, 624 insertions(+), 203 deletions(-)

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New package flowr with initial version 0.9.6.5
Package: flowr
Type: Package
Title: Streamlining Design and Deployment of Complex Workflows
Description: An interface to streamline design of complex workflows and their deployment to a High Performance Computing Cluster.
Version: 0.9.6.5
Depends: methods, stats, diagram
Imports: knitr, ggplot2, RSQLite, reshape2
Date: 2015-03-27
VignetteBuilder: knitr
URL: https://github.com/sahilseth/flowr
BugReports: https://github.com/sahilseth/flowr/issues
Authors@R: c(person("Sahil", "Seth", role = c("aut", "cre"), email = "me@sahilseth.com"))
License: MIT + file LICENSE
Packaged: 2015-03-28 01:20:25 UTC; sseth
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-29 01:24:16

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Package WGCNA updated to version 1.46 with previous version 1.43 dated 2015-01-15

Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder and Steve Horvath with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder

Diff between WGCNA versions 1.43 dated 2015-01-15 and 1.46 dated 2015-03-28

 WGCNA-1.43/WGCNA/R/smaFunctions-Rna.R       |only
 WGCNA-1.43/WGCNA/R/smaFunctions.R           |only
 WGCNA-1.43/WGCNA/man/na.Rd                  |only
 WGCNA-1.43/WGCNA/man/plotCor.Rd             |only
 WGCNA-1.43/WGCNA/man/plotMat.Rd             |only
 WGCNA-1.43/WGCNA/man/rgcolors.func.Rd       |only
 WGCNA-1.43/WGCNA/man/stat.diag.da.Rd        |only
 WGCNA-1.43/WGCNA/man/stats.bwss.Rd          |only
 WGCNA-1.46/WGCNA/Changelog                  |   33 ++++
 WGCNA-1.46/WGCNA/DESCRIPTION                |   10 -
 WGCNA-1.46/WGCNA/MD5                        |   41 ++---
 WGCNA-1.46/WGCNA/NAMESPACE                  |    3 
 WGCNA-1.46/WGCNA/R/Functions.R              |   50 ++++--
 WGCNA-1.46/WGCNA/R/blockwiseModulesC.R      |    6 
 WGCNA-1.46/WGCNA/R/consensusTOM.R           |    8 -
 WGCNA-1.46/WGCNA/R/empiricalBayesLM.R       |only
 WGCNA-1.46/WGCNA/R/exportFunctions.R        |   15 +-
 WGCNA-1.46/WGCNA/R/heatmapWithLegend.R      |    6 
 WGCNA-1.46/WGCNA/man/WGCNA-package.Rd       |   11 -
 WGCNA-1.46/WGCNA/man/bicovWeights.Rd        |only
 WGCNA-1.46/WGCNA/man/empiricalBayesLM.Rd    |only
 WGCNA-1.46/WGCNA/man/labeledHeatmap.Rd      |   15 +-
 WGCNA-1.46/WGCNA/man/qvalue.Rd              |    2 
 WGCNA-1.46/WGCNA/src/corFunctions-common.c  |   76 +++++-----
 WGCNA-1.46/WGCNA/src/corFunctions-common.h  |   10 -
 WGCNA-1.46/WGCNA/src/corFunctions-unified.c |  205 +++++++++++++++-------------
 WGCNA-1.46/WGCNA/src/networkFunctions.c     |    2 
 27 files changed, 293 insertions(+), 200 deletions(-)

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New package spgs with initial version 1.0
Package: spgs
Type: Package
Encoding: latin1
Title: Statistical Patterns in Genomic Sequences
Version: 1.0
Date: 2015-03-27
Authors@R: c(person("Andrew", "Hart", role = c("aut", "cre"), email = "ahart@dim.uchile.cl"), person("Servet", "Martínez", role = "aut"), person("Universidad de Chile", role = "cph"), person("INRIA-Chile", role = "cph"))
Author: Andrew Hart [aut, cre], Servet Martínez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
Maintainer: Andrew Hart
Copyright: Universidad de Chile, INRIA-Chile
Depends: R (>= 3.0)
Enhances: seqinr
Description: A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
License: GPL (>= 2)
NeedsCompilation: yes
Classification/MSC: 62F03, 62G10, 62M07, 62P10, 92D20
Packaged: 2015-03-28 01:05:50 UTC; ahart
Repository: CRAN
Date/Publication: 2015-03-28 07:40:29

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Package Exact updated to version 1.5 with previous version 1.4 dated 2013-07-22

Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables. Unconditional exact tests are often more powerful than conditional exact tests and asymptotic tests.
Author: Peter Calhoun
Maintainer: Peter Calhoun

Diff between Exact versions 1.4 dated 2013-07-22 and 1.5 dated 2015-03-28

 DESCRIPTION          |   11 -
 MD5                  |   16 -
 R/binomialCode.R     |  416 +++++++++++++++++++++++++--------------------------
 R/exact.test.R       |  134 ++++++++++++----
 R/fisher.2x2.R       |   37 ++--
 R/multinomialCode.R  |  209 ++++++++++++-------------
 R/power.exact.test.R |  113 ++++++-------
 man/Exact-package.Rd |   12 -
 man/exact.test.Rd    |    9 -
 9 files changed, 514 insertions(+), 443 deletions(-)

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