R help - Sep 2006 - problem coercing truncated character vector to levels

Dear R wizes,
 
I have a data.frame of species abundances with column names consisting
of 4 letter codes then an underscore and a number like this:
 
abco_1, abco_2, abco_3, psm_1, psme_2, psme_3, etc.
 
I would like to get an identifier for all the abco, and psme and other
species etc.
 
I used 
 
        spec.fact<-substring(names(spec.count),1,4)
 
To make a vector of the first 4 letters of each name. I tried using 
        spec.groups <- unique(spec.fact)
 
and then matching    
 
        pmatch(spec.groups[1],spec.fact)
 
to get out the indexes of all the columns that match the second unique
value, i.e what are the column number for all the abco columns.  Then I
could make a temporary data.frame of just the abco columns. I could loop
through the unique vector spec.groups to do this for each group and
perform the operations I need to on each individual mini-dataframe.
Unfortunately the matching doesn't work. Any suggestions?
 
Ken
 
 
 

Kenneth B. Pierce Jr.

Research Ecologist

Landscape Ecology, Modeling, Mapping and Analysis Team 

PNW Research Station - USDA-FS 

3200 SW Jefferson Way,  Corvallis,  OR 97331 

ken.pierce@oregonstate.edu

541 750-7393 

http://www.fsl.orst.edu/lemma/gnnfire

 

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Thanks. The problem is I have an variable number of these indices. I
have figured part of it out and it involves a code like this with the
indented column being the important one. Of course I work on this for 4
hours and figure part of it out about 2 minutes after posting. The
answer involves subsetting directly on a matched level value.
 
spec.fact<-substring(names(spec.count),1,4)
 
spec.col <- data.frame(ni(spec.count),spec.fact)
spec.fact2 <- factor(spec.fact)
spec.fact2
i<-7
        spec.sub<- spec.col[spec.col[,3]==levels(spec.fact2)[i],]
spec.wk <- frcheck[,spec.sub[,2]]
dim(spec.wk)
 
 
Ken

________________________________

From: nalluri pratap [mailto:pratap_stat@yahoo.co.in] 
Sent: Wednesday, September 20, 2006 4:03 PM
To: Pierce, Ken
Subject: Re: [R] problem coercing truncated character vector to levels


hi,
 
Try this one 
 
spec.count<- strtrim(c("abco_1", "abco_2",
"abco_3", "psm_1", "psme_2",
"psme_3"),c(4,4,4,3,4,4))
spec.groups <- unique(spec.count)
pmatch(spec.groups[1],spec.fact)
 
Thanks and Regards,
Pratap

"Pierce, Ken" <ken.pierce@oregonstate.edu> wrote:

	Dear R wizes,
	
	I have a data.frame of species abundances with column names
consisting
	of 4 letter codes then an underscore and a number like this:
	
	abco_1, abco_2, abco_3, psm_1, psme_2, psme_3, etc.
	
	I would like to get an identifier for all the abco, and psme and
other
	species etc.
	
	I used 
	
	spec.fact<-substring(names(spec.count),1,4)
	
	To make a vector of the first 4 letters of each name. I tried
using 
	spec.groups <- unique(spec.fact)
	
	and then matching 
	
	pmatch(spec.groups[1],spec.fact)
	
	to get out the indexes of all the columns that match the second
unique
	value, i.e what are the column number for all the abco columns.
Then I
	could make a temporary data.frame of just the abco columns. I
could loop
	through the unique vector spec.groups to do this for each group
and
	perform the operations I need to on each individual
mini-dataframe.
	Unfortunately the matching doesn't work. Any suggestions?
	
	Ken
	
	
	
	
	Kenneth B. Pierce Jr.
	
	Research Ecologist
	
	Landscape Ecology, Modeling, Mapping and Analysis Team 
	
	PNW Research Station - USDA-FS 
	
	3200 SW Jefferson Way, Corvallis, OR 97331 
	
	ken.pierce@oregonstate.edu
	
	541 750-7393 
	
	http://www.fsl.orst.edu/lemma/gnnfire
	
	
	
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