From: Petr PIKAL <petr.pikal_at_precheza.cz>

Date: Thu, 03 May 2007 08:47:54 +0200

xx

R-help_at_stat.math.ethz.ch 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. Received on Thu 03 May 2007 - 07:03:57 GMT

Date: Thu, 03 May 2007 08:47:54 +0200

r-help-bounces_at_stat.math.ethz.ch napsal dne 02.05.2007 16:47:55:

*>
*

> 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?
*

Well, it seems that you have the data which you want but why you do not see them is not clear for me.

I tried:

x<-sample(0:2, 100, replace=T)

dim(x)<-c(10,10)

x

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 0 1 0 0 1 1 1 1 0 1 [2,] 0 1 0 2 1 0 2 0 0 2 [3,] 0 2 0 0 0 1 1 0 1 2 ... [10,] 1 2 0 0 1 2 0 2 1 0xx<-data.frame(var=c("a", "b"),x)

xx

var X1 X2 X3 X4 X5 X6 X7 X8 X9 X10

1 a 0 1 0 0 1 1 1 1 0 1

2 b 0 1 0 2 1 0 2 0 0 2

....

9 a 1 1 0 1 1 0 0 2 2 0

10 b 1 2 0 0 1 2 0 2 1 0

dist(xx, method='euclidean', diag=F,upper=F)

1 2 3 4 5 6 7 8 9 2 2.966479 3 2.345208 3.146427 4 3.633180 3.633180 4.571652 5 4.195235 5.549775 4.571652 4.195235 6 4.195235 4.195235 4.062019 3.924283 3.924283 7 1.816590 3.781534 3.316625 3.781534 3.781534 4.8062468 2.774887 4.571652 3.633180 4.062019 4.062019 4.806246 3.316625 9 3.316625 4.449719 4.062019 4.449719 3.316625 4.449719 2.774887 3.146427

10 2.774887 5.029911 3.633180 4.324350 3.146427 4.324350 2.569047 2.966479 2.774887

xxx<-dist(xx, method='euclidean', diag=F,upper=F)
Warning message:

NAs introduced by coercion

str(xxx)

Class 'dist' atomic [1:45] 2.97 2.35 3.63 4.20 4.20 ...

..- attr(*, "Size")= int 10 ..- attr(*, "Diag")= logi FALSE ..- attr(*, "Upper")= logi FALSE ..- attr(*, "method")= chr "euclidean" ..- attr(*, "call")= language dist(x = xx, method = "euclidean", diag =F, upper = F)

seems to be similar to what you get. So I wonder why you do not see you matrix. Try dist.PxMx[1:50] or head(dist.PxMx) to see if you can get something from it.

Regards

Petr

*>
**>
**>
*

> 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?

*> >
**>
**> --
**> View this message in context: http://www.nabble.com/NAs-introduced-by-
**> coercion-in-dist%28%29-tf3680727.html#a10286882
**> Sent from the R help mailing list archive at Nabble.com.
**>
**> ______________________________________________
**> R-help_at_stat.math.ethz.ch 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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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. Received on Thu 03 May 2007 - 07:03:57 GMT

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