R help - Jun 2009 - wrong results when apply+sum with missing values (NA)

Hi all,

I can't compute the sum by columns to a matrix using apply() when I've
got
missing values (either 0 or NA)...
I've got this matrix:
>nafam
    Micro Flavo Helio Pseud Rhodo Bdello Chloro Syntro Verruco Prochloro
SAR11
I       1     1     1    NA    NA      1      3     NA       1         6
1
VII    NA     1     2     1    NA      2     16      1      NA        12
35
XI     NA    NA    NA    NA     1     NA      2     NA       1        17
94

and want to count the total frequencies by column, but I keep getting the
same output
>apply(nafam,2,sum,na.nr=T)
    Micro     Flavo     Helio     Pseud     Rhodo    Bdello    Chloro
Syntro
       NA        NA        NA        NA        NA        NA        22
NA
  Verruco Prochloro     SAR11
       NA        36       131

or this output with this other way:
> apply(nafam,2,sum,na.last=NA)
    Micro     Flavo     Helio     Pseud     Rhodo    Bdello    Chloro
Syntro
       NA        NA        NA        NA        NA        NA        NA
NA
  Verruco Prochloro     SAR11
       NA        NA        NA

I tried to change NA's to "0" and built this matrix:
> nafam[is.na(nafam)] <- 0
> nafam
    Micro Flavo Helio Pseud Rhodo Bdello Chloro Syntro Verruco Prochloro
SAR11
I       1     1     1     0     0      1      3      0       1         6
1
VII     0     1     2     1     0      2     16      1       0        12
35
XI      0     0     0     0     1      0      2      0       1        17
94

and then tried to sum again everything but the zeroes:
> apply(tfam>0,2,sum)
    Micro     Flavo     Helio     Pseud     Rhodo    Bdello    Chloro
Syntro
        1         2         2         1         1         2
3         1
  Verruco Prochloro     SAR11
        2         3         3

but the sums doesn't add correctly!!! (see Helio = 2 when it should be 3)
I do need to exclude the zeroes because I'm using the output fro plotting a
cumulative frequency distribution.

Any idea of why is this happening?

	[[alternative HTML version deleted]]

Where the <expletive deleted> did you get the argument ``na.nr''?
Perhaps you need new reading glasses.

Anyhow, unless there's something else you're not telling us,

	apply(nafam,2,sum,na.rm=TRUE)

should work just fine.

	cheers,

		Rolf Turner

On 17/06/2009, at 1:56 PM, Germ?n Bonilla wrote:
> Hi all,
>
> I can't compute the sum by columns to a matrix using apply() when  
> I've got
> missing values (either 0 or NA)...
> I've got this matrix:
>
>> nafam
>
>     Micro Flavo Helio Pseud Rhodo Bdello Chloro Syntro Verruco  
> Prochloro
> SAR11
> I       1     1     1    NA    NA      1      3     NA        
> 1         6
> 1
> VII    NA     1     2     1    NA      2     16      1       
> NA        12
> 35
> XI     NA    NA    NA    NA     1     NA      2     NA        
> 1        17
> 94
>
> and want to count the total frequencies by column, but I keep  
> getting the
> same output
>
>> apply(nafam,2,sum,na.nr=T)
>
>     Micro     Flavo     Helio     Pseud     Rhodo    Bdello    Chloro
> Syntro
>        NA        NA        NA        NA        NA        NA        22
> NA
>   Verruco Prochloro     SAR11
>        NA        36       131
>
> or this output with this other way:
>
>> apply(nafam,2,sum,na.last=NA)
>     Micro     Flavo     Helio     Pseud     Rhodo    Bdello    Chloro
> Syntro
>        NA        NA        NA        NA        NA        NA        NA
> NA
>   Verruco Prochloro     SAR11
>        NA        NA        NA
>
> I tried to change NA's to "0" and built this matrix:
>
>> nafam[is.na(nafam)] <- 0
>> nafam
>
>     Micro Flavo Helio Pseud Rhodo Bdello Chloro Syntro Verruco  
> Prochloro
> SAR11
> I       1     1     1     0     0      1      3      0        
> 1         6
> 1
> VII     0     1     2     1     0      2     16      1        
> 0        12
> 35
> XI      0     0     0     0     1      0      2      0        
> 1        17
> 94
>
> and then tried to sum again everything but the zeroes:
>
>> apply(tfam>0,2,sum)
>     Micro     Flavo     Helio     Pseud     Rhodo    Bdello    Chloro
> Syntro
>         1         2         2         1         1         2
> 3         1
>   Verruco Prochloro     SAR11
>         2         3         3
>
> but the sums doesn't add correctly!!! (see Helio = 2 when it should  
> be 3)
> I do need to exclude the zeroes because I'm using the output fro  
> plotting a
> cumulative frequency distribution.
>
> Any idea of why is this happening?
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
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