[Rflptools-commits] r18 - in pkg/RFLPtools: . inst/doc man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 13 22:17:37 CEST 2014
Author: stamats
Date: 2014-08-13 22:17:37 +0200 (Wed, 13 Aug 2014)
New Revision: 18
Modified:
pkg/RFLPtools/DESCRIPTION
pkg/RFLPtools/inst/doc/RFLPtools.pdf
pkg/RFLPtools/man/0RFLP-package.Rd
pkg/RFLPtools/man/FragMatch.Rd
pkg/RFLPtools/man/germ.Rd
pkg/RFLPtools/man/simulateRFLPdata.Rd
pkg/RFLPtools/vignettes/RFLPtools.Rnw
Log:
made some minor updates to prepare the release of 1.6 on CRAN
Modified: pkg/RFLPtools/DESCRIPTION
===================================================================
--- pkg/RFLPtools/DESCRIPTION 2014-03-02 19:32:36 UTC (rev 17)
+++ pkg/RFLPtools/DESCRIPTION 2014-08-13 20:17:37 UTC (rev 18)
@@ -2,8 +2,8 @@
Type: Package
Title: Tools to analyse RFLP data
Version: 1.6
-Date: 2014-03-02
-Author: Fabienne Flessa, Alexandra Kehl, Matthias Kohl
+Date: 2014-08-14
+Author: Fabienne Flessa, Alexandra Kehl, Mohammed Aslam Imtiaz, Matthias Kohl
Maintainer: Matthias Kohl <Matthias.Kohl at stamats.de>
Description: RFLPtools provides functions to analyse DNA fragment samples
(i.e. derived from RFLP-analysis) and standalone BLAST report files
Modified: pkg/RFLPtools/inst/doc/RFLPtools.pdf
===================================================================
(Binary files differ)
Modified: pkg/RFLPtools/man/0RFLP-package.Rd
===================================================================
--- pkg/RFLPtools/man/0RFLP-package.Rd 2014-03-02 19:32:36 UTC (rev 17)
+++ pkg/RFLPtools/man/0RFLP-package.Rd 2014-08-13 20:17:37 UTC (rev 18)
@@ -15,8 +15,8 @@
\tabular{ll}{
Package: \tab RFLPtools\cr
Version: \tab 1.6 \cr
-Date: \tab 2014-03-02 \cr
-Depends: \tab R(>= 3.0.0), stats, utils, grDevices, RColorBrewer\cr
+Date: \tab 2014-08-13 \cr
+Depends: \tab R(>= 3.0.0), stats, utils, graphics, grDevices, RColorBrewer\cr
Suggests: \tab lattice, MKmisc(>= 0.8)\cr
License: \tab LGPL-3\cr
}}
@@ -25,6 +25,7 @@
\author{
Fabienne Flessa \email{Fabienne.Flessa at uni-bayreuth.de},\cr
Alexandra Kehl \email{Alexandra.Kehl at botgarten.uni-tuebingen.de},\cr
+ Mohammed Aslam Imtiaz,\cr
Matthias Kohl \email{Matthias.Kohl at stamats.de}\cr
\emph{Maintainer:} Matthias Kohl \email{Matthias.Kohl at stamats.de}
Modified: pkg/RFLPtools/man/FragMatch.Rd
===================================================================
--- pkg/RFLPtools/man/FragMatch.Rd 2014-03-02 19:32:36 UTC (rev 17)
+++ pkg/RFLPtools/man/FragMatch.Rd 2014-08-13 20:17:37 UTC (rev 18)
@@ -39,7 +39,7 @@
Mycorrhiza 2007, 17:133-136
}
\author{
- Matthias Kohl \email{Matthias.Kohl at stamats.de}
+ Mohammed Aslam Imtiaz, Matthias Kohl \email{Matthias.Kohl at stamats.de}
}
%\note{}
\seealso{ \code{\link{newDataGerm}}, \code{\link{refDataGerm}} }
Modified: pkg/RFLPtools/man/germ.Rd
===================================================================
--- pkg/RFLPtools/man/germ.Rd 2014-03-02 19:32:36 UTC (rev 17)
+++ pkg/RFLPtools/man/germ.Rd 2014-08-13 20:17:37 UTC (rev 18)
@@ -39,7 +39,7 @@
Mycorrhiza 2003, 13:171-172.
}
\author{
- Matthias Kohl \email{Matthias.Kohl at stamats.de}
+ Mohammed Aslam Imtiaz, Matthias Kohl \email{Matthias.Kohl at stamats.de}
}
%\note{}
\seealso{ \code{\link{newDataGerm}}, \code{\link{refDataGerm}} }
Modified: pkg/RFLPtools/man/simulateRFLPdata.Rd
===================================================================
--- pkg/RFLPtools/man/simulateRFLPdata.Rd 2014-03-02 19:32:36 UTC (rev 17)
+++ pkg/RFLPtools/man/simulateRFLPdata.Rd 2014-08-13 20:17:37 UTC (rev 18)
@@ -43,7 +43,7 @@
}
%\references{}
\author{
- Matthias Kohl \email{Matthias.Kohl at stamats.de}
+ Mohammed Aslam Imtiaz, Matthias Kohl \email{Matthias.Kohl at stamats.de}
}
%\note{}
\seealso{ \code{\link{RFLPdata}}, \code{\link{RFLPref}} }
Modified: pkg/RFLPtools/vignettes/RFLPtools.Rnw
===================================================================
--- pkg/RFLPtools/vignettes/RFLPtools.Rnw 2014-03-02 19:32:36 UTC (rev 17)
+++ pkg/RFLPtools/vignettes/RFLPtools.Rnw 2014-08-13 20:17:37 UTC (rev 18)
@@ -42,7 +42,7 @@
University of Bayreuth, 95440 Bayreuth, Germany, Fabienne.Flessa at uni-bayreuth.de},
A. Kehl\thanks{Botanical Garden, University of Tübingen, Hartmeyerstr.\ 123, 72076 Tübingen,
Germany, Alexandra.Kehl at botgarten.uni-tuebingen.de} and
-M. Kohl\thanks{Department of Mechanical and Process Engineering,
+M. Kohl\thanks{Department of Medical and Life Sciences,
Furtwangen University, 78054 VS-Schwenningen, Germany, Matthias.Kohl at stamats.de}\\ \\
\includegraphics[width = 3cm]{logoUBT.png}
\includegraphics[width = 3cm]{logoTueb.png}
@@ -59,7 +59,9 @@
sizes (i.e. derived from RFLP-analysis)
\item the analysis of standalone BLAST report files (i.e. DNA sequence analysis)
\end{itemize}
-In this short vignette we describe and demonstrate the available functions.
+see also \cite{Flessa13}.
+In this short vignette we describe and demonstrate the available functions. We
+start with loading the package.
<<load>>=
library(RFLPtools)
@
@@ -309,6 +311,16 @@
%-------------------------------------------------------------------------------
\begin{thebibliography}{1}
+ \bibitem{Flessa13}
+ Flessa, Fabienne; Kehl, Alexandra; Kohl, Matthias.
+ \newblock Analysing diversity and community structures using PCR-RFLP: a new software application".
+ \newblock Molecular Ecology Resources 2013 Jul; 13(4):726-33.
+
+ \bibitem{Matsumoto96}
+ Matsumoto, Masaru; Furuya, Naruto; Takanami, Yoichi; Matsuyama, Nobuaki.
+ \newblock RFLP analysis of the PCR-amplified 28S rDNA in Rhizoctonia solani.
+ \newblock Mycoscience 1996 37:351 - 356
+
\bibitem{Poussier00}
Poussier, Stephane; Trigalet-Demery, Danielle; Vandewalle, Peggy; Goffinet, Bruno;
Luisetti, Jacques; Trigalet, Andre.
@@ -317,11 +329,6 @@
an African subdivision.
\newblock Microbiology 2000 146:1679-1692
- \bibitem{Matsumoto96}
- Matsumoto, Masaru; Furuya, Naruto; Takanami, Yoichi; Matsuyama, Nobuaki.
- \newblock RFLP analysis of the PCR-amplified 28S rDNA in Rhizoctonia solani.
- \newblock Mycoscience 1996 37:351 - 356
-
\end{thebibliography}
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