[R] Re: Need help on how to list functions from a loaded package...

Sean Davis sdavis2 at mail.nih.gov
Tue Jan 20 19:14:17 CET 2004


where PKGNAME is the name of an installed library.


Note that you can also use:

help.start() to get html help (assuming your browswer is configured).

----- Original Message -----
From: "rex_bryan at urscorp.com" <rexbryan1 at comcast.net>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, January 20, 2004 12:16 PM
Subject: [R] Re: Need help on how to list functions from a loaded package...

> To All
> How does one get a list of functions from a loaded package so that one can
> then get the appropriate help for each of the functions.  Currently my
> method is
> based on a lot of trial-and-error.
> Here's an example of what I mean...
> >From this forum I learn that an interesting package called "multtest"
> on Bioconductor.
> I then use R Console's "Packages" -- "Install package(s)  from
> to
> download "multtest".  I then load "multtest" into my session using
> "Packages -- Load package..."
> I now want to investigate what functions exist in "multtest".
> >?package:multtest
> Error in "?"(package:multtest) : Object "package" not found
> > help("multtest")
> Error in help("multtest") : No documentation for `multtest' in specified
> packages and libraries:
>   you could try `help.search("multtest")'
> >help.search("multtest")
> ------------R Information Window ------------------------------
> Help files with alias or title matching 'multtest' using fuzzy matching:
> eff.aovlist(base)                 Compute Efficiencies of Multistratum
> Analysis of Variance
> dataDensityString(Hmisc)          Internal Hmisc functions
> .mt.BLIM(multtest)                Internal multtest functions and
> SSI(spatial)                      Simulates Sequential Spatial Inhibition
> Point Process
> Strauss(spatial)                  Simulates Strauss Spatial Point Process
> Type 'help(FOO, package = PKG)' to inspect entry 'FOO(PKG) TITLE'.
> -------------------------------------------------------------------
> Oh Oh... I've met this FOO before...and I don't have a clue on how to
> interpret this message.  So I'm
> at a loss of how to ask about what is in the "multtest" package unless I
> back to the original source
> on the Web.  By visiting
> http://www.bioconductor.org/repository/release1.3/package/html/graph.html
> the multtest package consists of...
> --------- snip
> multtest     Multiple Testing Procedures 1.3.3
> ----------snip
>       Function Description
>       golub Gene expression dataset from Golub et al. (1999)
>       mt.maxT Step-down maxT and minP multiple testing procedures
>       mt.plot Plotting results from multiple testing procedures
>       mt.rawp2adjp Adjusted p-values for simple multiple testing
>       mt.reject Identity and number of rejected hypotheses
>       mt.sample.teststat Permutation distribution of test statistics and
> (unadjusted) p-values
>       mt.teststat Computing test statistics for each row of a data frame
> ------------snip
> With the information on what the function names are, I can now use the "?"
> command on each of these functions.
> But I have a feeling that there is a better way ...Oh FOO
> --------------------------------------------
> Message: 33
> Date: Tue, 20 Jan 2004 01:58:20 +0100
> From: Tobias Sing <tsing at mpi-sb.mpg.de>
> Subject: Re: [R] graph algorithms in R
> To: rxg218 at psu.edu
> Cc: r-help at stat.math.ethz.ch
> Message-ID: <200401200158.20341.tsing at mpi-sb.mpg.de>
> Content-Type: text/plain;  charset="iso-8859-1"
> > I was wondering if there are any packages available that can represent
> > mathematical graphs along with functions to manipulate them? Google
> > did'nt turn up anything ( I may be asking too much of R :-/ )
> I was looking for the same thing the other day, and found that a graph
> package
> for R is being developed as part of the bioconductor project. However, I
> haven't tried it yet, so I don't know about the status (judging from the
> function list one shouldn't expect a comprehensive collection of graph
> algorithms, but at least the base structures and some random graph stuff
> seem
> to be implemented already). There is also a package for visualization,
> Rgraphviz.
> http://www.bioconductor.org/
> http://www.bioconductor.org/repository/release1.3/package/html/graph.html
> l
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