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

[Peter Solymos]

Hi All,

maybe a more transparent solution for the zombie factor problem
(dropping unused factor levels) for data frames is (note, this applies
for all factors in the data frame x):

x[] <- lapply(x, function(x) x[drop = TRUE])

As I recall, on the help page of factor(), there is a slight warning
against character or numeric coercion of factors.

Cheers,

Peter


On Sat, Nov 29, 2008 at 9:25 AM,  <byrnes at msi.ucsb.edu> wrote:
> 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
>>>
>>
>
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