I'm trying to run a very simple non-metric multidimensional scaling code on
a 8x5 character matrix.
gr T C M B
arcor 6 4 6 5
corfo 24 21 23 24
corma 25 15 26 17
crust 3 2 6 5
fil 15 12 15 15
fol 11 9 6 8
leat 10 11 13 13
seag 2 2 2 2
My code is as follows;
coma<-read.csv("coma.csv",header=TRUE)
coma.x<-as.matrix(coma)
coma.dist <- dist(coma.x) # right here I get a warning message -> In
dist(coma.x) : NAs introduced by coercion
WHAT DOES THAT MEAN??? the table has values and there are not NAs. Could
this be a by product of the way I inserted the data?
Please help.
--
Simona Augyte, MS
PhD student
Ecology and Evolutionary Biology
University of Connecticut
cell 707-832-7007
[[alternative HTML version deleted]]
HI,
coma<- read.table(text="
gr T C M B
arcor 6 4 6 5
corfo 24 21 23 24
corma 25 15 26 17
crust 3 2 6 5
fil 15 12 15 15
fol 11 9 6 8
leat 10 11 13 13
seag 2 2 2 2
",sep="",header=TRUE)
?coma.x<- as.matrix(coma)
str(coma.x)
# chr [1:8, 1:5] "arcor" "corfo" "corma"
"crust" "fil" "fol" ...
# - attr(*, "dimnames")=List of 2
#? ..$ : NULL
#? ..$ : chr [1:5] "gr" "T" "C" "M" ...
coma.dist<- dist(coma.x)
#Warning message:
#In dist(coma.x) : NAs introduced by coercion
?dist() #documentation
# dist(x, method = "euclidean", diag = FALSE, upper = FALSE, p = 2)
# x: a numeric matrix, data frame or ?"dist"? object.
?coma.x<- as.matrix(coma[,-1]) #####
?str(coma.x)
# int [1:8, 1:4] 6 24 25 3 15 11 10 2 4 21 ...
# - attr(*, "dimnames")=List of 2
?# ..$ : NULL
?# ..$ : chr [1:4] "T" "C" "M" "B"
?coma.dist<- dist(coma.x)
A.K.
----- Original Message -----
From: Simona Augyte <simona.augyte at uconn.edu>
To: r-help at r-project.org
Cc:
Sent: Saturday, August 31, 2013 6:30 PM
Subject: [R] NMDS QUESTION
I'm trying to run a very simple non-metric multidimensional scaling code on
a 8x5 character matrix.
gr T C M B
arcor 6 4 6 5
corfo 24 21 23 24
corma 25 15 26 17
crust 3 2 6 5
fil 15 12 15 15
fol 11 9 6 8
leat 10 11 13 13
seag 2 2 2 2
My code is as follows;
coma<-read.csv("coma.csv",header=TRUE)
coma.x<-as.matrix(coma)
coma.dist <- dist(coma.x) # right here I get a warning message -> In
dist(coma.x) : NAs introduced by coercion
WHAT DOES THAT MEAN??? the table has values and there are not NAs. Could
this be a by product of the way I inserted the data?
Please help.
--
Simona Augyte, MS
PhD student
Ecology and Evolutionary Biology
University of Connecticut
cell 707-832-7007
??? [[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.
On 01-09-2013, at 00:30, Simona Augyte <simona.augyte at uconn.edu> wrote:> I'm trying to run a very simple non-metric multidimensional scaling code on > a 8x5 character matrix. > gr T C M B > arcor 6 4 6 5 > corfo 24 21 23 24 > corma 25 15 26 17 > crust 3 2 6 5 > fil 15 12 15 15 > fol 11 9 6 8 > leat 10 11 13 13 > seag 2 2 2 2 > > My code is as follows; > coma<-read.csv("coma.csv",header=TRUE) > coma.x<-as.matrix(coma) > coma.dist <- dist(coma.x) # right here I get a warning message -> In > dist(coma.x) : NAs introduced by coercion > > WHAT DOES THAT MEAN??? the table has values and there are not NAs. Could > this be a by product of the way I inserted the data? >Yes. Your table contains characters and not numbers. Tell read.csv that the first column contains row names (assuming that that is indeed the case). coma<- read.csv(text=" gr T C M B arcor 6 4 6 5 corfo 24 21 23 24 corma 25 15 26 17 crust 3 2 6 5 fil 15 12 15 15 fol 11 9 6 8 leat 10 11 13 13 seag 2 2 2 2 ",sep="",row.names=1,header=TRUE) coma str(coma) dist(coma) Berend> Please help. > > -- > > Simona Augyte, MS > PhD student > Ecology and Evolutionary Biology > University of Connecticut > cell 707-832-7007 > > [[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.