R help - Jun 2009 - Problem in 'Apply' function: does anybody have other solution

Dear All,
  I am having some problem in apply function.
I have some data like below. I want to get a range vector (which is max-min
value for each row , ignoring NA values.)
> Species.all[1:10,]
       V2     V3     V4     V5    V6   V7    V8   V9
1   57543  55938  47175  54922 36032 5785 29497 7286
2   42364  40472  29887  40107 19723 2691 14445 3258
3   19461  19646  18538  22392  6744  794  4919 1024
4      45     41     28     34    33   NA    26   NA
5      45     41     28     34    33   NA    26   NA
6      45     41     28     34    33   NA    26   NA
7      14      9     14     14     7   NA    10   NA
8      20     25     10     15    21   NA    10   NA
9      20     25     10     15    21   NA    10   NA
10    578    566    478    753   361  150   262  170
> dim(Species.all)
[1] 1862    8

I used apply function like below. I used this same function for some other
data, there it worked. But here its not working (giving error message).
> Range.j=apply(Species.all,1,max,na.rm TRUE)-apply(Species.all,1,min,na.rm =
TRUE)
Error in apply(Species.all, 1, max, na.rm = TRUE) - apply(Species.all,  :
    non-numeric argument to binary operator

When i tried to check, you can see from the steps it is giving totally wrong
results.
> apply(Species.all[1:10,],1,max)
     1      2      3      4      5      6      7      8      9     10
"7286" "3258" "1024"     NA     NA     NA     NA  
NA     NA " 753"
> apply(Species.all[1:10,],1,min)
       1        2        3        4        5        6        7
8        9       10
" 47175" " 29887" " 18538"       NA       NA      
NA       NA
NA       NA  "  262"


Main problem is, this code is working for some cases, but not for all. Does
any body have an idea, why it is so? Or can anyone show me some other way to
do the same.
Thanks in advance,
With best regard,
Suparna

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Dear All,
 Just to add some more lines in my previous query I am writing this. I was
checking with several data. The cases where the apply function is working,
the part of result looks like :
> apply(Species.all[1:10,],1,max,na.rm=TRUE)
    1     2     3     4     5     6     7     8     9    10
22392    45    45    45    14    25    25   753   101    10

and with the problematic data it looks like:
> apply(Species.all[1:10,],1,max,na.rm=TRUE)
     1      2      3      4      5      6      7      8      9     10
"7286" "3258" "1024"  " 45"  "
45"  " 45"   " 9"  " 25"  " 25"
" 753"

But my all the datasets are in CSV format. I am reading those datasets as
read.csv or read.delim
Can anybody please suggest me how to this problem?
Thanks and regards,
Suparna.


On Wed, Jun 17, 2009 at 1:14 PM, suparna mitra
<suparna.mitra@googlemail.com
> wrote:
> Dear All,
>   I am having some problem in apply function.
> I have some data like below. I want to get a range vector (which is max-min
> value for each row , ignoring NA values.)
> > Species.all[1:10,]
>        V2     V3     V4     V5    V6   V7    V8   V9
> 1   57543  55938  47175  54922 36032 5785 29497 7286
> 2   42364  40472  29887  40107 19723 2691 14445 3258
> 3   19461  19646  18538  22392  6744  794  4919 1024
> 4      45     41     28     34    33   NA    26   NA
> 5      45     41     28     34    33   NA    26   NA
> 6      45     41     28     34    33   NA    26   NA
> 7      14      9     14     14     7   NA    10   NA
> 8      20     25     10     15    21   NA    10   NA
> 9      20     25     10     15    21   NA    10   NA
> 10    578    566    478    753   361  150   262  170
> > dim(Species.all)
> [1] 1862    8
>
> I used apply function like below. I used this same function for some other
> data, there it worked. But here its not working (giving error message).
>
> > Range.j=apply(Species.all,1,max,na.rm >
TRUE)-apply(Species.all,1,min,na.rm = TRUE)
> Error in apply(Species.all, 1, max, na.rm = TRUE) - apply(Species.all,  :
>     non-numeric argument to binary operator
>
> When i tried to check, you can see from the steps it is giving totally
> wrong results.
>
> > apply(Species.all[1:10,],1,max)
>      1      2      3      4      5      6      7      8      9     10
> "7286" "3258" "1024"     NA     NA     NA    
NA     NA     NA " 753"
> > apply(Species.all[1:10,],1,min)
>        1        2        3        4        5        6        7
> 8        9       10
> " 47175" " 29887" " 18538"       NA       NA 
NA       NA
> NA       NA  "  262"
>
>
> Main problem is, this code is working for some cases, but not for all. Does
> any body have an idea, why it is so? Or can anyone show me some other way
to
> do the same.
> Thanks in advance,
> With best regard,
> Suparna
>
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David Winsemius' solution:

 
> apply(data.matrix(df), 1, I)
   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]

x    1    2    3    4    5    6    7    8    9    10

y    1    3    4    5    6    7    8    9   10     2

 

For y and [,2] above the value is 3. Why is the value not 2? 

It looks like the value is 2 for y and [,10] (this should be 10, right?)

and values 3 to 10 are shifted one position to the left for "y".

 

I got the same results when I ran this code.

 

Thanks,

 

Jude

 

David Winsemius wrote:

 

On Jun 17, 2009, at 9:27 AM, jim holtman wrote:

 
> Do an 'str' of your object.  It looks like one of the columns is  
> probably
> character/factor since there are quotes around the 'numbers'.  You
> can also
> explicity convert the offending columns to numeric is you want to.   
> Also use
> colClasses on the read.csv to define the class of the data in each  
> column.
> This will should you where the error is.
 

One function that might be of use is data.matrix which will attempt to  

convert character vectors to numeric vectors across an entire  

dataframe. I hope this is not beating a dead horse, but see if these  

examples are helpful in any way:

 

 > ?data.matrix

 > df <- data.frame(x=1:10,y=as.character(1:10))

 > df

     x  y

1   1  1

2   2  2

3   3  3

4   4  4

5   5  5

6   6  6

7   7  7

8   8  8

9   9  9

10 10 10    # .... not all is as it seems

 > apply(df,1,I)

   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]

x " 1" " 2" " 3" " 4" " 5"
" 6" " 7" " 8" " 9" "10"

y "1"  "2"  "3"  "4"  "5" 
"6"  "7"  "8"  "9"  "10"

 > df2 <- data.frame(x=1:10,y=1:10)

 > apply(df2,1,I)

   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]

x    1    2    3    4    5    6    7    8    9    10

y    1    2    3    4    5    6    7    8    9    10

 > str(df)

'data.frame':     10 obs. of  2 variables:

  $ x: int  1 2 3 4 5 6 7 8 9 10

  $ y: Factor w/ 10 levels
"1","10","2","3",..: 1 3 4 5 6 7 8 9 10
2

 

# so that's weird. y isn't even a character vector !?!? Such are the  

strange beasts called factors.

 

# solution? or at least one strategy

 

 > apply(data.matrix(df), 1, I)

   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]

x    1    2    3    4    5    6    7    8    9    10

y    1    3    4    5    6    7    8    9   10     2

 

 

 

 

___________________________________________
Jude Ryan
Director, Client Analytical Services
Strategy & Business Development
UBS Financial Services Inc.
1200 Harbor Boulevard, 4th Floor
Weehawken, NJ 07086-6791
Tel. 201-352-1935
Fax 201-272-2914
Email: jude.ryan at ubs.com



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Several folks pointed out the problem is most likely that a column of 
data is being read in as a factor.

I prefer to solve this by setting as.is=TRUE as one of the arguments to 
read.table() (unless I am mis-remembering and it needs to be set to 
FALSE :-) ).  The point is to tell the read function to read character 
strings in as character strings, rather than converting them into factors.
After that you can convert the offending column with as.numeric or one 
of the date-conversion functions (if the input is date/time strings)

Carl