R help - Jun 2006 - can I call user-created functions without source() ?

Hi,

I have to R fairly recently from Matlab, where I have been used to
organising my own custom functions into directories which are adding to
the Matlab search path. This enables me to call them as I would one of
Matlab's built-in functions. I have not found a way of doing the same
thing in R. I have resorted to using source() on symlinks located in the
current directory. Not very satisfactory.

I looked at the R homepage and considered making a "package" of my
commonly used functions so that I can call them in one go:
library(myFuncions, lib.loc="/path/to/library") Perhaps this is the
only
solution but the docs on the web make the process seem rather
complicated--I only have a few script files I want to call! Surely
there's a straightforward solution?

How have other people solved this problem? Perhaps someone has a simple
"package skeleton" into which I can drop my scripts?


Thanks,

Rob



-- 
  Rob Campbell   -   Research Student
 Autistic Bacteriophage Research Group
 www.autisticBacteriophage.notlong.com

               Oxford

      www.robertcampbell.co.uk

On 19-Jun-06 Rob Campbell wrote:
> Hi,
> 
> I have to R fairly recently from Matlab, where I have been used to
> organising my own custom functions into directories which are adding to
> the Matlab search path. This enables me to call them as I would one of
> Matlab's built-in functions. I have not found a way of doing the same
> thing in R. I have resorted to using source() on symlinks located in
> the
> current directory. Not very satisfactory.
> 
> I looked at the R homepage and considered making a "package" of
my
> commonly used functions so that I can call them in one go:
> library(myFuncions, lib.loc="/path/to/library") Perhaps this is
the
> only
> solution but the docs on the web make the process seem rather
> complicated--I only have a few script files I want to call! Surely
> there's a straightforward solution?
> 
> How have other people solved this problem? Perhaps someone has a simple
> "package skeleton" into which I can drop my scripts?
> 
> 
> Thanks,
> 
> Rob
There are pros and cons to this, but on the whole I sympathise
with you (having pre-R been a heavy matlab/octave user myself).

Unfortunately (from this perspective) R does not seem to have
an automatic "load-on-demand" facility similar to what happens
in matlab (i.e. you call a function by name, and R would search
for it in whatever the current search-path is, and load its
definition plus what else it depends on).

I have a few definitions which I want in every R session, so
I have put these in my ".Rprofile". But this is loaded from
my home directory, not from the directory where I was when I
started R, so it is the same every time. Again, one of the
conveniences of the matlab/octave approach is that you can
have a different sub-directory for each project, so if you
start work in a particular one then you have access to any
special definitions for that project, and not to others.

I'm no expert on this aspect of R, but I suspect that the way
start-up is organised in R does not fit well with the other
kind of approach. I stand to be corrected, of course ...

And others may well have formulated their own neat work-rounds,
so we wait eagerly to hear about these!

Best wishes,
Ted.

--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at nessie.mcc.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 19-Jun-06                                       Time: 11:25:15
------------------------------ XFMail ------------------------------

On 6/19/2006 5:36 AM, Rob Campbell wrote:
> Hi,
> 
> I have to R fairly recently from Matlab, where I have been used to
> organising my own custom functions into directories which are adding to
> the Matlab search path. This enables me to call them as I would one of
> Matlab's built-in functions. I have not found a way of doing the same
> thing in R. I have resorted to using source() on symlinks located in the
> current directory. Not very satisfactory.
> 
> I looked at the R homepage and considered making a "package" of
my
> commonly used functions so that I can call them in one go:
> library(myFuncions, lib.loc="/path/to/library") Perhaps this is
the only
> solution but the docs on the web make the process seem rather
> complicated--I only have a few script files I want to call! Surely
> there's a straightforward solution?
> 
> How have other people solved this problem? Perhaps someone has a simple
> "package skeleton" into which I can drop my scripts?
You could try the "package.skeleton" function.  It's not
completely
painless (you are still expected to edit some of the files, and to 
install the package), but it's not really so bad.  There are plans 
(already partially implemented in R-devel) to make it easier for the 
next release.  (So far I think the change is to require less editing on 
the default generated files.)

To answer the more general question: I generally use two styles of 
development.  For things where have long term usefulness, I go through 
the work above and create a package.  For more ephemeral things, I put 
them in a file, and in the file where I'm working on today's script, I 
put in source("blahblah.R") at the beginning.

You can also use a file named .Rprofile to contain commands to run; it 
is searched for in the current directory, then the user's home 
directory.  So you could put your source("blahblah.R") into .Rprofile
if
you want these functions to always be available.

Duncan Murdoch

Rob,

I accomplish what you ask by putting my functions into a dedicated 
directory, starting R there and sourcing them, and loading the resulting 
workspace in .Rprofile with this:

attach("d:/R/MHP/MHPmisc/.RData")

I find that procedure simpler than learning the package mechanism.  It 
is easy to add new functions periodically.

Not long ago, I posted the R code I used to automate the process.  As 
the archive seems unreachable right now (from here, anyway) and the code 
is relatively short, I'll post it again:

##########################################################
## 00make.r       MHP      Dec 2005
## This R script clears the current workspace, sources all R scripts
## found in the working directory, and then saves the workspace for
## use in other R sessions.

# Clear all existing objects in workspace:
rm(list=ls())

# Make a list of all R source files in this directory:
flist = list.files(path=".", pattern=".+\.r")

# Remove from the list all files containing the string "00":
# Such files should be used for temporary funcs:
flist2 = flist[-grep("00",flist)]

# Source the files:
for (i in 1:length(flist2)) {
   cat("Sourcing", flist2[i],"\n")
   source(flist2[i])
   }
# Remove temporary objects:
rm(i,flist,flist2)
# Save workspace:
save.image()
# Write message to user:
cat("\nNOTE: The workspace has been saved with all functions.\n",
    "     When exiting R, please do NOT save again.\n")
ls()
##########################################################

I run that script straight from the (Windows) command line with the 
following shell script:

rterm.exe --no-restore --no-save < 00make.r > 00make.txt

You will probably need to modify that slightly to work under Unix/Linux.

Hope that helps.

...Mike



on 6/19/2006 5:36 AM Rob Campbell said the following:
> Hi,
>
> I have to R fairly recently from Matlab, where I have been used to
> organising my own custom functions into directories which are adding to
> the Matlab search path. This enables me to call them as I would one of
> Matlab's built-in functions. I have not found a way of doing the same
> thing in R. I have resorted to using source() on symlinks located in the
> current directory. Not very satisfactory.
>
> I looked at the R homepage and considered making a "package" of
my
> commonly used functions so that I can call them in one go:
> library(myFuncions, lib.loc="/path/to/library") Perhaps this is
the only
> solution but the docs on the web make the process seem rather
> complicated--I only have a few script files I want to call! Surely
> there's a straightforward solution?
>
> How have other people solved this problem? Perhaps someone has a simple
> "package skeleton" into which I can drop my scripts?
>
>
> Thanks,
>
> Rob
>   
-- 
Michael Prager, Ph.D.
Southeast Fisheries Science Center
NOAA Center for Coastal Fisheries and Habitat Research
Beaufort, North Carolina  28516
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