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
On Wed, Jun 17, 2009 at 7:41 AM, suparna mitra <
mi...@informatik.uni-tuebingen.de> wrote:
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.mi...@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
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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