[R] NAs introduced by coercion in dist()

[Silvia Lomascolo]

It was suggested that the 'NAs introduced by coercion' message might be
warning me that my data are not what they should be.  I checked this using
str(PeaksMatrix), as suggested, and the data seem to be what I thought they
were: 

'data.frame':   335 obs. of  127 variables:
 $ Code   : Factor w/ 335 levels "A1MR","A1MU",..: 1 2 3 4 5 6 7 8 9 10 ...
 $ P3.70  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ P3.97  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ P4.29  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ P4.90  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ P6.30  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ P6.45  : num  7.73 0 0 0 0 0 4.03 0 0 0 ...
 $ P6.55  : num  0 0 0 0 0 0 0 0 0 0 ...

...

I do have 335 observations, 127 variables that are named P3.70, 3.97, P4.29,
etc..  This was a relief, but I still don't know whether the distance matrix
is what it should be.  I tried 'str(dist.PxMx)', which is the name of my
distance matrix, but I get something that has not much meaning to me, an
unexperienced R user:

Class 'dist'  atomic [1:55945] 329.6 194.9 130.1  70.7 116.9 ...
  ..- attr(*, "Size")= int 335
  ..- attr(*, "Labels")= chr [1:335] "1" "2" "3" "4" ...
  ..- attr(*, "Diag")= logi FALSE
  ..- attr(*, "Upper")= logi FALSE
  ..- attr(*, "method")= chr "euclidean"
  ..- attr(*, "call")= language dist(x = PeaksMatrix, method = "euclidean",
diag = FALSE, upper = FALSE,      p = 2)

Any more suggestions, please?



Silvia Lomascolo wrote:
> 
> I work with Windows and use R version 2.4.1. I am JUST starting to learn
> this program...
> 
> I get this warning message 'NAs introduced by coercion' while trying to
> build a distance matrix (to be analyzed with NMDS later) from a 336 x 100
> data matrix.  The original matrix has lots of zeros and no missing values,
> but I don't think this should matter.
> 
> I searched this forum and people have suggested that the warning should be
> ignored but when I try to print the distance matrix I only get the row
> numbers (the matrix seems to be 'empty') and I'm not being able to judge
> whether the matrix worked or not.
> 
> To get the distance matrix I wrote:
> dist.PxMx <- dist (PeaksMatrix, method='euclidean', diag=FALSE,
> upper=FALSE)
> 
> I tried including the p argument (included in the help for dist()) and
> leaving it out, but that didn't seem to change anything.  I think that's
> required for one distance measure though, not for euclidean dist. 
> 
> Should I really ignore this warning? If so, why am I not being able to see
> the distance matrix?
> 

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