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error with persp()- increasing 'x' and 'y' values expected

5 messages · adick, David Winsemius, David L Carlson

Original
adick
# 
I want to use persp to graph my data and it keeps giving me the error 
increasing 'x' and 'y' values expected, even though my data is in increasing
order with respect to x and y.

Here is the code I'm currently using: 
bob= scan ("SBA3dataTaxonB.txt",what="char")
labels = bob[1:3]
bob=bob[-c(1,2,3)]
bob=as.numeric(bob)
bob=array(bob,dim=c(3, length(bob)/3))
bob=t(bob)
data.frame(bob) -> bob
bob = bob[order(bob[,1], bob[,3]),]
persp(bob[,1], bob[,3], bob[,2], log="bob[,1]")

The first few lines of the txt file SBA3dataTaxonB.txt look like this:
variable	TaxonB	central
10	19	0.002
10	25	0.002
10	26	0.002
1	17	0.002
1	23	0.002
1	16	0.002
0.1	48	0.002
0.1	47	0.002
0.1	57	0.002
10	15	0.004
10	22	0.004
10	22	0.004
1	21	0.004
1	22	0.004
1	27	0.004
0.1	73	0.004
0.1	62	0.004

Can anyone help me figure out why I am getting this error? And also a
possible solution would be greatly appreciated.
-Thanks, Amanda

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David Winsemius
#
On Feb 20, 2012, at 2:15 PM, adick wrote:

            

      
      
      
    

        
Do you have missing entries? (Running your data fragment through your  
code produces the same error.) You may want to use rep with each and  
times arguments to construct a regular grid and then population the  
missing entries in  matrix with NA's.

            

      
      
      
    

        
Any way .... The z argument to `persp` is supposed to be a matrix of  
dimension == length(x)*length(y):

?matrix

            

      
      
      
    

        

      
      
    

        
David Winsemius, MD
West Hartford, CT

  
  


  


      

    

    

      
      

        


  

        

      adick
    

    

      
      #
    

  


  

      
On Feb 20, 2012, at 2:15 PM, adick wrote:

        
Do you have missing entries? (Running your data fragment through your  
code produces the same error.) You may want to use rep with each and  
times arguments to construct a regular grid and then population the  
missing entries in  matrix with NA's.



Yes, there are missing entries. I don't know what rep and times arguments
are or how to do anything you just said, because I'm knew to R.

I did however figure out how to take the average of my three replicates and
try to plot that, which returns the same error. Here is the updated code:

bob= scan ("SBA3dataTaxonB.txt",what="char")
labels = bob[1:3]
bob=bob[-c(1,2,3)]
bob=as.numeric(bob)
bob=array(bob,dim=c(3, length(bob)/3))
bob=t(bob)
data.frame(bob) -> bob
vary=0
varx= 0
varz=0

for (r in 1:(length(bob[,1])/3)) {
    vary[r] <- mean(bob[(1+((r-1)*3)):(3+((r-1)*3)),2])
    varx[r] <- bob[(1+((r-1)*3)),1]
    varz[r] <- bob[(1+((r-1)*3)),3]
}
rob <- data.frame(varx=varx,varz=varz,vary=vary)

rob = rob[order(rob[,1], rob[,2]),]
persp(rob[,1], rob[,2], rob[,3], log="rob[,1]")



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      David Winsemius
    

    

      
      #
    

  


  

      
On Feb 20, 2012, at 5:49 PM, adick wrote:

        

            

      
      
      
    

        
?rep

 > rep(1:3, times=3)
[1] 1 2 3 1 2 3 1 2 3
 > rep(1:3, each=3)
[1] 1 1 1 2 2 2 3 3 3

You can also use gl

?gl

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      David L Carlson
    

    

      
      #
    

  


  

      
You do not have your data organized in a way that persp() can use it. Here
is a simple example. The function will not work with x, y, z vectors. X and
Y are vectors in order with no repeated values, Z is a matrix containing one
value for every combination of x and y:

            

      
      
      
    

        
You must define a grid and specify a single value at each point on that
grid. 

----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of David Winsemius
Sent: Monday, February 20, 2012 10:09 PM
To: adick
Cc: r-help at r-project.org
Subject: Re: [R] error with persp()- increasing 'x' and 'y' values expected

        
On Feb 20, 2012, at 5:49 PM, adick wrote:

        

            

      
      
      
    

        
?rep

 > rep(1:3, times=3)
[1] 1 2 3 1 2 3 1 2 3
 > rep(1:3, each=3)
[1] 1 1 1 2 2 2 3 3 3

You can also use gl

?gl