[Bioc-devel] How to do permutations, combinations, intergrations, differentiations

Lazarus Mramba LMramba at kilifi.kemri-wellcome.org
Tue Dec 5 12:08:51 CET 2006

I also would wish to know how to do permutation and Combination,
Factorials, How to intergrate and differentiate equations using the R
environment as a calculator.
Please advise
Lazarus Mramba

>>> bioc-devel-request at stat.math.ethz.ch 12/05 2:00 PM >>>
Send Bioc-devel mailing list submissions to
	bioc-devel at stat.math.ethz.ch 

To subscribe or unsubscribe via the World Wide Web, visit
or, via email, send a message with subject or body 'help' to
	bioc-devel-request at stat.math.ethz.ch 

You can reach the person managing the list at
	bioc-devel-owner at stat.math.ethz.ch 

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Bioc-devel digest..."

Today's Topics:

   1. Re: Sweave changes (keep.source = TRUE or FALSE?) (Seth Falcon)


Message: 1
Date: Mon, 04 Dec 2006 16:10:01 -0800
From: Seth Falcon <sfalcon at fhcrc.org>
Subject: Re: [Bioc-devel] Sweave changes (keep.source = TRUE or
To: bioc-devel at stat.math.ethz.ch 
Cc: friedrich.leisch at stat.uni-muenchen.de,	Duncan Murdoch
	<murdoch at stats.uwo.ca>
Message-ID: <m27ix7ryna.fsf_-_ at ziti.local>
Content-Type: text/plain; charset=us-ascii

[I've moved this discussion to bioc-devel where it began and
belongs.  For those catching up, Fritz Leisch wrote some comments
about recent Sweave changes (mostly quoted below) and Duncan Murdoch
responded.  I have some comments added below.]

Duncan Murdoch <murdoch at stats.uwo.ca> writes:
> On 12/3/2006 11:55 AM, Friedrich Leisch wrote:
>> [ To Bioc-Core: This continues a discussion in R-core on the
>> Duncan Murdoch made to the parser and Sweave to keep original
>> formatting and comments of code chunks. ]
>> Sorry to join in late, I was travelling last week. First, let me
>> Duncan for his work, this really fixes one of the main drawbacks
>> Sweave had!
>> Hence, I agree with Duncan and Martin in that I would like to
>> the default in R to keep.source=TRUE. But I understand Robert that
>> testing software gets hard if the tools which are used for testing
>> change.
>> As discussed by email this summer on r-devel I want to change
>> Sweave default for 2.5: I want to set stylepath=FALSE and include
>> \usepackage{/path/to/Sweave.sty} by default. This means in effect
>> each Sweave file needs to be adapted, by either inserting
>> \usepackage{Sweave} or \SweaveOpts{stylepath=true} in the header. I
>> didn't implement the changes back then because the discussion was
>> close to feature freeze.
>> I also will do some other Sweave changes over christmas break, but
>> those should all be safe, i.e., only add functionality.
>> Before people now start yelling at me: We can only improve
>> if we are allowed to change it and/or fix behavior that can be
>> considered a bug. And the paths inserted on Windows machines in an
>> English locale are buggy (and were so ever since ...).
>> To make future changes easier I want to suggest the following (for
>> BioC): Have all package authors insert a
>> 	\SweaveInput{BiocSweaveDefaults}
>> at the beginning of each vignette, and centrally provide a
>> BiocSweaveDefaults.Rnw file with settings we think are appropriate
>> BioC (details to be discussed). With that we would have easy means
>>  1) changing Sweave when necessary, but
>>  2) keeping defaults in sync for all BioC vignettes, and overriding
>>     changes we don't like.
>> If we include the usapackage{Sweave} statement in
>> BiocSweaveDefaults.Rnw, we have central control for all Sweave
>> processing options as well as for latex options like noae or nogin.
>> Comments?
> I think that looks like a good long-term solution.  For 2.5.0, would
> be possible to put in place a way to change SweaveOpts defaults in
> vignettes with *no* changes to the vignettes?  I.e. some sort of
> external config file which set the defaults for any SweaveOpts
> I'd suggest the search order for this file should be
>    - a location specified in the Sweave call
>    - the directory of the .Rnw file
>    - the home directory of the current user
>    - a new RHOME/share/Sweave directory, or possibly
> Duncan Murdoch

I like the idea of being able to modify SweaveOpts without having to
change the vignette contents.  For this to be usable for us, it needs
to get picked up by 'R CMD build', at least, because that is how
vignettes get built in our build system.

A central BiocSweaveDefaults.Rnw file could be more trouble than it is
worth.  It requires modifying all vignettes to include the file and
then there is the question of where such a file would live.
Generally, developers only maintain a single package and don't do a
checkout of everything.  Right now, packages are self-contained and I
would hate to see that change.  -- but I think something along these
lines could provide useful insulation against changes in Sweave that
we aren't ready for.

+ seth

Duncan M. and Fritz: perhaps you guys could subscribe to bioc-devel
for a short period of time so your messages will go through?


Bioc-devel mailing list
Bioc-devel at stat.math.ethz.ch 

End of Bioc-devel Digest, Vol 33, Issue 1

More information about the Bioc-devel mailing list