[R-sig-eco] Subset by family name?

[byrnes at msi.ucsb.edu]

This can still be a problem after subsetting with zombie factors hanging
around.  It's particularly annoying when your boxplotting from a subset,
as you'll have a bunch of empty entries in the plot.  I have a function I
call purgef that deals with eliminating levels of a factor that I have
subsetted out.

purgef<-function(x){
  x<-as.character(x)
  x<-as.factor(x)
  return(x)
}

Gets rid of those pesky zombie levels.

In your case

Yut_are$Mark<-purgef(Yut_are$Mark)

> Sorry to bother everyone---I realized I should have used "==" instead
> of "=" in the subset syntax!
>
>
> Quoting Ophelia Wang <opheliawang at mail.utexas.edu>:
>
>> Hi all,
>>
>> I thought this should be very simple, but I'm not sure where the
>> problem is. I have a .txt data file that contains X and Y coordinates
>> of trees and their family names:
>>
>> "X"	"Y"	"Mark"
>> 0	28	"Sapotaceae"
>> 1	30	"Meliaceae"
>> 1	40	"Meliaceae"
>> 1	60	"Mimosaceae"
>> 1	76	"Olacaceae"
>> 1.5	73	"Myristicaceae"
>> 2	34	"Euphorbiaceae"
>> 2	62	"Olacaceae"
>> 2	86	"Mimosaceae"
>> 2.5	36	"Arecaceae"
>> 3	22	"Nyctaginaceae"
>> 3	25	"Moraceae"
>> 3	38	"Rubiaceae"
>> 3	47	"Desconocido "
>> 3	99	"Mimosaceae"
>> 3.5	24	"Anacardiaceae"
>> 3.5	57	"Sapotaceae"
>> 4	1	"Lecythidaceae"
>>
>> Now I just want to work on one family for various spatial analyses in
>> ads and spatstats, so I wrote:
>>
>> Yut <-read.delim(
>> "C:/dissertation/data2006/Parcela_1-3/Yutsun_tree.txt", header = TRUE,
>> sep = "\t", quote="\"", dec=".", fill = TRUE )
>>
>> Yut_are <- subset (Yut, Mark="Arecaceae", select=c(X, Y, Mark))
>>
>> However, the summary of Yut_are still contains trees of other families:
>>
>>   X                Y                    Mark
>>  Min.   :  0.00   Min.   : 0.00   Myristicaceae: 65
>>  1st Qu.: 24.00   1st Qu.:24.00   Lecythidaceae: 60
>>  Median : 46.00   Median :51.00   Sapotaceae   : 51
>>  Mean   : 48.07   Mean   :49.72   Moraceae     : 45
>>  3rd Qu.: 72.50   3rd Qu.:75.50   Arecaceae    : 41
>>  Max.   :100.00   Max.   :99.00   Mimosaceae   : 34
>>                                   (Other)      :313
>>
>> Please tell me how do I subset a dataset like this to extract trees
>> from only one or a few families? Thanks a lot!
>>
>> Ophelia
>>
>