From noreply at r-forge.r-project.org Wed Aug 13 22:17:37 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 13 Aug 2014 22:17:37 +0200 (CEST) Subject: [Rflptools-commits] r18 - in pkg/RFLPtools: . inst/doc man vignettes Message-ID: <20140813201737.5FB3F186250@r-forge.r-project.org> 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 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 T?bingen, Hartmeyerstr.\ 123, 72076 T?bingen, 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. <>= 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} %------------------------------------------------------------------------------- \end{document}