R help - Jan 2004 - 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

help(package=PKGNAME)
library(help=PKGNAME)

where PKGNAME is the name of an installed library.

help(package=multtest)
library(help=multtest)

Note that you can also use:

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

Sean
----- 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"
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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http://www.R-project.org/posting-guide.html
>