[Seqinr-commits] r1797 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 6 19:38:40 CEST 2014
Author: jeanlobry
Date: 2014-06-06 19:38:39 +0200 (Fri, 06 Jun 2014)
New Revision: 1797
Modified:
www/src/mainmatter/introduction.rnw
www/src/mainmatter/introduction.tex
Log:
compil 3.0-11 and url fix for db growth
Modified: www/src/mainmatter/introduction.rnw
===================================================================
--- www/src/mainmatter/introduction.rnw 2014-06-06 17:16:14 UTC (rev 1796)
+++ www/src/mainmatter/introduction.rnw 2014-06-06 17:38:39 UTC (rev 1797)
@@ -5,6 +5,7 @@
\author{Lobry, J.R.}
\begin{document}
+\SweaveOpts{concordance=TRUE}
\SweaveInput{../config/commonrnw.rnw}
\maketitle
\tableofcontents
@@ -143,7 +144,6 @@
{
nm <- nm + length(grep("http:", tmp[dtab[i]:ftab[i]]))
}
- nm <- nm / 2
return( list( nm = nm, nc = length(dtab) ) )
}
@
@@ -170,15 +170,10 @@
Previous versions of \Rlogo{} and packages are available on CRAN mirrors,
for instance at \url{http://cran.univ-lyon1.fr/src/contrib/Archive}.
}.
-The last compiled version of this document is distributed along with the \seqinr{}
-package in the \texttt{/doc} folder. Once \seqinr{} has been installed, the
-full path to the package is given by the following \Rlogo{} code :
+The last compiled version of this document is available at the \seqinr{}
+home page at \url{http://seqinr.r-forge.r-project.org/.}
-<<whereiseqinr,fig=F>>=
-.find.package("seqinr")
-@
-
\section{About sequin and \seqinr{}}
Sequin is the well known sofware used to submit sequences to GenBank, \seqinr{}
Modified: www/src/mainmatter/introduction.tex
===================================================================
--- www/src/mainmatter/introduction.tex 2014-06-06 17:16:14 UTC (rev 1796)
+++ www/src/mainmatter/introduction.tex 2014-06-06 17:38:39 UTC (rev 1797)
@@ -6,6 +6,7 @@
\usepackage{Sweave}
\begin{document}
+\input{introduction-concordance}
%
% To change the R input/output style:
%
@@ -126,37 +127,36 @@
\begin{Schunk}
\begin{Sinput}
- acnucbooksize <- 4.5
- acnucbp <- 526506
- mybank <- choosebank("genbank")
+ acnucbooksize <- 4.5 # cm
+ acnucbp <- 526506 # bp
+ choosebank("genbank") -> mybank
closebank()
mybank$details
\end{Sinput}
\begin{Soutput}
-[1] " **** ACNUC Data Base Content **** "
-[2] " GenBank Rel. 174 (15 October 2009) Last Updated: Nov 5, 2009"
-[3] "108,943,317,873 bases; 111,355,981 sequences; 7,239,424 subseqs; 573,990 refers."
-[4] "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
+[1] " **** ACNUC Data Base Content **** "
+[2] " GenBank Release 201 (15 April 2014) Last Updated: Jun 2, 2014"
+[3] "160,671,579,040 bases; 172,482,713 sequences; 18,666,226 subseqs; 786,167 refers."
+[4] "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
\end{Soutput}
\begin{Sinput}
- bpbk <- unlist(strsplit(mybank$details[3], split = " "))[1]
+ unlist(strsplit(mybank$details[3], split=" "))[1] -> bpbk
bpbk
\end{Sinput}
\begin{Soutput}
-[1] "108,943,317,873"
+[1] "160,671,579,040"
\end{Soutput}
\begin{Sinput}
- bpbk <- as.numeric(paste(unlist(strsplit(bpbk, split = ",")),
- collapse = ""))
- widthcm <- acnucbooksize * bpbk/acnucbp
+ bpbk <- as.numeric(paste(unlist(strsplit(bpbk, split = ",")), collapse = ""))
+ widthcm <- acnucbooksize*bpbk/acnucbp
(widthkm <- widthcm/10^5)
\end{Sinput}
\begin{Soutput}
-[1] 9.311289
+[1] 13.73246
\end{Soutput}
\end{Schunk}
-It would be about 9.3
+It would be about 13.7
kilometer long in ACNUC book format to print GenBank today (\today). As a
matter of comparison, our local universitary library buiding\footnote{
Université de Lyon, F-69000, Lyon ; Université Lyon 1 ;
@@ -183,9 +183,9 @@
The Comprehensive \Rlogo{} Archive Network, CRAN, is a network of servers
around the world that store identical, up-to-date, versions of code and documentation
for R. At compilation time of this document, there were
-68
+95
mirrors available
-from 34 countries.
+from 45 countries.
Please use the CRAN mirror nearest to you to minimize network load, they are
listed at \texttt{http://cran.r-project.org/mirrors.html}, and can be directly
selected with the function \texttt{chooseCRANmirror()}.
@@ -195,27 +195,17 @@
In the terminology of the \Rlogo{} project \cite{R, RfromR}, this document
is a package \emph{vignette}, which means that all code outputs present
here were actually obtained by runing them.
-The examples given thereafter were run under \texttt{R version 2.10.0 (2009-10-26)}
-on Thu Nov 5 11:14:18 2009 with Sweave \cite{Sweave}. There is a section at the end of
+The examples given thereafter were run under \texttt{R version 3.1.0 (2014-04-10)}
+on Fri Jun 6 19:34:34 2014 with Sweave \cite{Sweave}. There is a section at the end of
each chapter called \textbf{Session Informations} that gives details about
packages and package versions that were involved\footnote{
Previous versions of \Rlogo{} and packages are available on CRAN mirrors,
for instance at \url{http://cran.univ-lyon1.fr/src/contrib/Archive}.
}.
-The last compiled version of this document is distributed along with the \seqinr{}
-package in the \texttt{/doc} folder. Once \seqinr{} has been installed, the
-full path to the package is given by the following \Rlogo{} code :
+The last compiled version of this document is available at the \seqinr{}
+home page at \url{http://seqinr.r-forge.r-project.org/.}
-\begin{Schunk}
-\begin{Sinput}
- .find.package("seqinr")
-\end{Sinput}
-\begin{Soutput}
-[1] "/Users/lobry/seqinr/pkg.Rcheck/seqinr"
-\end{Soutput}
-\end{Schunk}
-
\section{About sequin and \seqinr{}}
Sequin is the well known sofware used to submit sequences to GenBank, \seqinr{}
@@ -251,9 +241,9 @@
lseqinr()[1:9]
\end{Sinput}
\begin{Soutput}
-[1] "a" "aaa" "AAstat" "acnucclose"
-[5] "acnucopen" "al2bp" "alllistranks" "alr"
-[9] "amb"
+[1] "a" "aaa" "aacost" "aaindex"
+[5] "AAstat" "acnucclose" "acnucopen" "al2bp"
+[9] "alllistranks"
\end{Soutput}
\end{Schunk}
@@ -303,7 +293,7 @@
Do not re-invent (there's a patent \cite{wheel} on it anyway).
At the compilation time of this document there were
-2028
+5098
contributed packages available. Even if you don't want to be spoon-feed
\textit{{\`a} bouche ouverte},
it's not a bad
@@ -397,10 +387,8 @@
\begin{Schunk}
\begin{Sinput}
- tablecode(numcode = 3, latexfile = "../tables/code3.tex",
- size = "small")
- tablecode(numcode = 4, latexfile = "../tables/code4.tex",
- size = "small")
+ tablecode(numcode = 3, latexfile = "../tables/code3.tex", size = "small")
+ tablecode(numcode = 4, latexfile = "../tables/code4.tex", size = "small")
\end{Sinput}
\end{Schunk}
@@ -427,32 +415,33 @@
\begin{Sinput}
data <- get.db.growth()
scale <- 1
- ltymoore <- 1
- date <- data$date
- Nucleotides <- data$Nucleotides
- Month <- data$Month
- plot.default(date, log10(Nucleotides), main = "Update of Fig. 1 from Lobry (2004) LNCS, 3039:679:\nThe exponential growth of genome sequence data",
- xlab = "Year", ylab = "Log10 number of nucleotides", pch = 19,
- las = 1, cex = scale, cex.axis = scale, cex.lab = scale)
- abline(lm(log10(Nucleotides) ~ date), lwd = 2)
- lm1 <- lm(log(Nucleotides) ~ date)
- mu <- lm1$coef[2]
- dbt <- log(2)/mu
- dbt <- 12 * dbt
- x <- mean(date)
- y <- mean(log10(Nucleotides))
- a <- log10(2)/1.5
- b <- y - a * x
- lm10 <- lm(log10(Nucleotides) ~ date)
- for (i in seq(-10, 10, by = 1)) if (i != 0) abline(coef = c(b +
- i, a), col = "black", lty = ltymoore)
+ ltymoore <- 1 # line type for Moore's law
+ date <- data$date
+ Nucleotides <- data$Nucleotides
+ Month <- data$Month
+ plot.default(date, log10(Nucleotides),
+ main = "Update of Fig. 1 from Lobry (2004) LNCS, 3039:679:\nThe exponential growth of genome sequence data", xlab = "Year",
+ ylab = "Log10 number of nucleotides", pch = 19, las = 1,
+ cex = scale, cex.axis = scale, cex.lab = scale)
+ abline(lm(log10(Nucleotides) ~ date), lwd = 2)
+ lm1 <- lm(log(Nucleotides) ~ date)
+ mu <- lm1$coef[2]
+ dbt <- log(2)/mu
+ dbt <- 12 * dbt
+ x <- mean(date)
+ y <- mean(log10(Nucleotides))
+ a <- log10(2)/1.5
+ b <- y - a * x
+ lm10 <- lm(log10(Nucleotides) ~ date)
+ for (i in seq(-10, 10, by = 1)) if (i != 0)
+ abline(coef = c(b + i, a), col = "black", lty = ltymoore)
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/introduction-dbg}
\setkeys{Gin}{width=0.8\textwidth}
-The doubling time is now 16.9 months.
+The doubling time is now 18.3 months.
\begin{figure}
@@ -484,20 +473,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}\raggedright
- \item R version 2.10.0 (2009-10-26), \verb|i386-apple-darwin8.11.1|
- \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item R version 3.1.0 (2014-04-10), \verb|x86_64-apple-darwin13.1.0|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8|
\item Base packages: base, datasets, graphics, grDevices, grid,
methods, stats, utils
- \item Other packages: ade4~1.4-13, ape~2.4, grImport~0.4-4,
- MASS~7.3-3, quadprog~1.4-11, seqinr~2.0-7, tseries~0.10-21,
- XML~2.6-0, xtable~1.5-5, zoo~1.5-8
- \item Loaded via a namespace (and not attached): gee~4.13-14,
- lattice~0.17-26, nlme~3.1-96, tools~2.10.0
+ \item Other packages: ade4~1.6-2, ape~3.1-2, grImport~0.9-0,
+ MASS~7.3-31, seqinr~3.0-11, tseries~0.10-32, XML~3.98-1.1,
+ xtable~1.7-3
+ \item Loaded via a namespace (and not attached): lattice~0.20-29,
+ nlme~3.1-117, quadprog~1.5-5, tools~3.1.0, zoo~1.7-11
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Nov 5 11:14:20 2009
+ \item \Rlogo{} compilation time was: Fri Jun 6 19:34:40 2014
\item \LaTeX{} compilation time was: \today
\end{itemize}
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