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

[Huntsinger, Reid]

You can get help on the whole package by 

> help(package="multtest")

which is likely pretty close to what you want. There's the index etc for the
package on the web as well. You can also just look in the package's
installation directory. If it's loaded you can do an ls(2) say if it loaded
in position 2, to get all objects in the package.

Reid

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of rex_bryan at urscorp.com
Sent: Tuesday, January 20, 2004 12:17 PM
To: r-help at stat.math.ethz.ch
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"
exists
on Bioconductor.
I then use R Console's "Packages" -- "Install package(s)  from Bioconductor"
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 variables
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 go
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 procedures
      mt.reject Identity and number of rejected hypotheses
      mt.sample.teststat Permutation distribution of test statistics and raw
(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

REX
--------------------------------------------

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
http://www.bioconductor.org/repository/release1.2/package/html/Rgraphviz.htm
l

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