R help - Dec 2007 - Sweave : change value in rnw file to generate multiple "single" reports ?

Hello,

I'm still trying to make the life of my colleagues easier. Nice, isn't
it ?
At the moment, I'm looking for a way to generate multiple "single
report".
In fact I have a .rnw file which send a query to a MySQL database
(rs<-dbSendQuery(con, statement="select * from treatdata where
name='Device1'")

But of course my colleagues have many devices and don't want to enter the
rnw file to change the name of the device.

Is there a way to pass arguments to Sweave like Sweave("myfile.rnw",
namevar="Device2") and it will change namevar by Device2 into the file
myfile.rnw before creating the .tex file ?
Or is it possible to do it via another language, that is: loading the rnw
file, modifying it, saving it and finally calling Sweave ?

Whatever the solution, I need you help. In advance thank you.
Ptit Bleu.   
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The ability to pass arguments on the

R CMD Sweave

line is something I would very much like to have as well.

Currently you need to create a shell or batch file that accepts
the arguments, place those into environment variables using shell
or batch code and then run sweave.  R code in your swevae file
would then read the environment variables using Sys.getenv.

On Dec 10, 2007 11:25 AM, Ptit_Bleu <ptit_bleu at yahoo.fr>
wrote:
>
> Hello,
>
> I'm still trying to make the life of my colleagues easier. Nice,
isn't it ?
> At the moment, I'm looking for a way to generate multiple "single
report".
> In fact I have a .rnw file which send a query to a MySQL database
> (rs<-dbSendQuery(con, statement="select * from treatdata where
> name='Device1'")
>
> But of course my colleagues have many devices and don't want to enter
the
> rnw file to change the name of the device.
>
> Is there a way to pass arguments to Sweave like
Sweave("myfile.rnw",
> namevar="Device2") and it will change namevar by Device2 into the
file
> myfile.rnw before creating the .tex file ?
> Or is it possible to do it via another language, that is: loading the rnw
> file, modifying it, saving it and finally calling Sweave ?
>
> Whatever the solution, I need you help. In advance thank you.
> Ptit Bleu.
> --
> View this message in context:
http://www.nabble.com/Sweave-%3A-change-value-in-rnw-file-to-generate-multiple-%22single%22-reports---tp14256204p14256204.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

I think something like this would work.

Change your query to 

rs <- dbSendQuery(con, statement = paste("select * from treatdata where
name='", whichDevice,"'", sep = ""))

And then create a script like.

whichDevice <- "Device1"
Sweave("myfile.rnw")
whichDevice <- "Device2"
Sweave("myfile.rnw")

HTH,

Thierry

------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx op inbo.be 
www.inbo.be 

Do not put your faith in what statistics say until you have carefully
considered what they do not say.  ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney

-----Oorspronkelijk bericht-----
Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org]
Namens Ptit_Bleu
Verzonden: maandag 10 december 2007 17:26
Aan: r-help op r-project.org
Onderwerp: [R] Sweave : change value in rnw file to generate multiple
"single"reports ?


Hello,

I'm still trying to make the life of my colleagues easier. Nice, isn't
it ?
At the moment, I'm looking for a way to generate multiple "single
report".
In fact I have a .rnw file which send a query to a MySQL database
(rs<-dbSendQuery(con, statement="select * from treatdata where
name='Device1'")

But of course my colleagues have many devices and don't want to enter
the
rnw file to change the name of the device.

Is there a way to pass arguments to Sweave like Sweave("myfile.rnw",
namevar="Device2") and it will change namevar by Device2 into the file
myfile.rnw before creating the .tex file ?
Or is it possible to do it via another language, that is: loading the
rnw
file, modifying it, saving it and finally calling Sweave ?

Whatever the solution, I need you help. In advance thank you.
Ptit Bleu.   
-- 
View this message in context:
http://www.nabble.com/Sweave-%3A-change-value-in-rnw-file-to-generate-mu
ltiple-%22single%22-reports---tp14256204p14256204.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
R-help op r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Within or before SWeave, you can use R.
Hence you can write some R function that first changes the rnw and runs 
SWeave thereafter, or even better, write something in your SWeave code 
that reads a user customized variables, e.g. from an environment 
variable or from some text file.

Uwe Ligges



Ptit_Bleu wrote:
> Hello,
> 
> I'm still trying to make the life of my colleagues easier. Nice,
isn't it ?
> At the moment, I'm looking for a way to generate multiple "single
report".
> In fact I have a .rnw file which send a query to a MySQL database
> (rs<-dbSendQuery(con, statement="select * from treatdata where
> name='Device1'")
> 
> But of course my colleagues have many devices and don't want to enter
the
> rnw file to change the name of the device.
> 
> Is there a way to pass arguments to Sweave like
Sweave("myfile.rnw",
> namevar="Device2") and it will change namevar by Device2 into the
file
> myfile.rnw before creating the .tex file ?
> Or is it possible to do it via another language, that is: loading the rnw
> file, modifying it, saving it and finally calling Sweave ?
> 
> Whatever the solution, I need you help. In advance thank you.
> Ptit Bleu.

Ptit_Bleu <ptit_bleu <at> yahoo.fr> writes:

... 
> Is there a way to pass arguments to Sweave like
Sweave("myfile.rnw",
> namevar="Device2") and it will change namevar by Device2 into the
file
> myfile.rnw before creating the .tex file ?
> Or is it possible to do it via another language, that is: loading the rnw
> file, modifying it, saving it and finally calling Sweave ?

You can set an environment variable in the system (SET DELTA=...), and read it
in from R:

Sys.getenv("DELTA") 

Works for Windows with a rather inconsistent implementation of environment
strings, so it should work the better with Linux.

Dieter

On 12/10/2007 11:25 AM, Ptit_Bleu wrote:
> Hello,
> 
> I'm still trying to make the life of my colleagues easier. Nice,
isn't it ?
> At the moment, I'm looking for a way to generate multiple "single
report".
> In fact I have a .rnw file which send a query to a MySQL database
> (rs<-dbSendQuery(con, statement="select * from treatdata where
> name='Device1'")
> 
> But of course my colleagues have many devices and don't want to enter
the
> rnw file to change the name of the device.
> 
> Is there a way to pass arguments to Sweave like
Sweave("myfile.rnw",
> namevar="Device2") and it will change namevar by Device2 into the
file
> myfile.rnw before creating the .tex file ?
Not as far as I know, but you could wrap Sweave() in another function 
that uses save() to write a file of variables, and start your .Rnw file 
with load("file.Rdata").
> Or is it possible to do it via another language, that is: loading the rnw
> file, modifying it, saving it and finally calling Sweave ?
Surely yes, there are lots of ways to automatically edit a text file.

Duncan Murdoch
> 
> Whatever the solution, I need you help. In advance thank you.
> Ptit Bleu.

Others have given some good advice, and what works best for you will
depend on exactly what you want to do and how you think about the
problem.  Here are just a couple of other ideas to throw into the mix.

If you want to edit the .rnw file, then the tools sed, awk, or perl (or
probably several others) can all do this quite easily.  For example if
you have a file (base.rnw) that has MYDEVICE everywhere that you want to
replace with Device2 or whatever then the following command at a command
prompt will create a new file (dev2.rnw) that is a copy of base.rnw with
all occurences of MYDEVICE replaced with Device2:

 perl -pe "s/MYDEVICE/Device2/g" base.rnw > dev2.rnw

Another tool that you may want to learn is "make".  You can set up a
makefile that shows how each file relates to the next in a chain of
steps, then just type something like:

 make device2.pdf

At the command line and it will automatically make the changes to your
.rnw file and possibly to data or other files involved, then run all the
steps needed to create device2.pdf, then deletes all the intermediate
files that you don't need (device2.dvi, ...).  It also has the benefit
of being able to update all the appropriate files when you update a data
file, script file, or .rnw file.

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
(801) 408-8111
 
 
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Ptit_Bleu
> Sent: Monday, December 10, 2007 9:26 AM
> To: r-help at r-project.org
> Subject: [R] Sweave : change value in rnw file to generate 
> multiple "single" reports ?
> 
> 
> Hello,
> 
> I'm still trying to make the life of my colleagues easier. 
> Nice, isn't it ?
> At the moment, I'm looking for a way to generate multiple 
> "single report".
> In fact I have a .rnw file which send a query to a MySQL 
> database (rs<-dbSendQuery(con, statement="select * from 
> treatdata where
> name='Device1'")
> 
> But of course my colleagues have many devices and don't want 
> to enter the rnw file to change the name of the device.
> 
> Is there a way to pass arguments to Sweave like
Sweave("myfile.rnw",
> namevar="Device2") and it will change namevar by Device2 into 
> the file myfile.rnw before creating the .tex file ?
> Or is it possible to do it via another language, that is: 
> loading the rnw file, modifying it, saving it and finally 
> calling Sweave ?
> 
> Whatever the solution, I need you help. In advance thank you.
> Ptit Bleu.   
> --
> View this message in context: 
> http://www.nabble.com/Sweave-%3A-change-value-in-rnw-file-to-g
> enerate-multiple-%22single%22-reports---tp14256204p14256204.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Dear Uwe,

Could you please give me the name of the function to open, to modify and to
save a r script ?
Just the name and I will look for the way to use them.

And if you have a link explaining how to use user customized variables from
an environment variable, it will be very helpful (as it is completely new to
me).

Thanks in advance,
Ptit Bleu.

------------------------------------------------


Within or before SWeave, you can use R.
Hence you can write some R function that first changes the rnw and runs 
SWeave thereafter, or even better, write something in your SWeave code 
that reads a user customized variables, e.g. from an environment 
variable or from some text file.

Uwe Ligges
-- 
View this message in context:
http://www.nabble.com/Sweave-%3A-change-value-in-rnw-file-to-generate-multiple-%22single%22-reports---tp14256204p14275809.html
Sent from the R help mailing list archive at Nabble.com.