Skip to content

filled contour plot with contour lines

8 messages · Peter Ehlers, Steve_Friedman at nps.gov, Clint Bowman +2 more

Steve_Friedman at nps.gov
# 
I'm stumped,  can anyone find my error in this sequence.

 for(j in 1:(varsize[4]-1))
      temp <- get.var.ncdf(nc=input,
varid="p_foraging",c(1,1,j),c(varsize[1],varsize[2],1))
         filled.contour(x, y, temp, color = terrain.colors,
             plot.title = title(main = paste("Everglades Wood Stork
Foraging Potential \nYear", (2000+j)),
             xlab = "UTM East", ylab = "UTM North") ,
             plot.axes = { contour(temp, add=T)
                axis(1, seq(450000 , 580000, by = 10000))
                axis(2, seq(2800000,4000000, by = 10000)) },
             key.title = title(main="Probability") ,
             key.axes = axis(4, seq(0 , 1 , by = 0.1))


The routine will work in a modified form without adding the coordinates
(the axis lines) but when I include these the routine produces various
errors, such as "dimension mismatch", or "unexpected end encountered."

I tried to follow the example on filled.contour help page.

Thanks in advance
   Steve

Steve Friedman Ph. D.
Ecologist  / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034

Steve_Friedman at nps.gov
Office (305) 224 - 4282
Fax     (305) 224 - 4147
Peter Ehlers
# 
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:

  for(j in 1:(varsize[4]-1)) { loop stuff }

Peter Ehlers
On 2011-04-01 11:48, Steve_Friedman at nps.gov wrote:
Steve_Friedman at nps.gov
# 
Hi Peter,

Thanks for taking the time to consider the problem. I realize the procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in size to
pull data into this process. Nobody in their right mind should work with
such things. It's a spatial temporal database with 10 years of daily data
in a irregular area spanning 405 x 287 cells.

Anyway, I tried your suggestion adding a { in front of the for loop and a
closing } following the last line.

It did not work.

Steve Friedman Ph. D.
Ecologist  / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034

Steve_Friedman at nps.gov
Office (305) 224 - 4282
Fax     (305) 224 - 4147


                                                                           
             Peter Ehlers                                                  
             <ehlers at ucalgary.                                             
             ca>                                                        To 
                                       "Steve_Friedman at nps.gov"            
             04/01/2011 05:08          <Steve_Friedman at nps.gov>            
             PM                                                         cc 
                                       "r-help at r-project.org"              
                                       <r-help at r-project.org>              
                                                                   Subject 
                                       Re: [R] filled contour plot with    
                                       contour lines                       
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:

  for(j in 1:(varsize[4]-1)) { loop stuff }

Peter Ehlers
On 2011-04-01 11:48, Steve_Friedman at nps.gov wrote:
http://www.R-project.org/posting-guide.html
Steve_Friedman at nps.gov
# 
Hi Peter,

Thanks for taking the time to consider the problem. I realize the procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in size to
pull data into this process. Nobody in their right mind should work with
such things. It's a spatial temporal database with 10 years of daily data
in a irregular area spanning 405 x 287 cells.

Anyway, I tried your suggestion adding a { in front of the for loop and a
closing } following the last line.

It did not work.


Steve Friedman Ph. D.
Ecologist  / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034

Steve_Friedman at nps.gov
Office (305) 224 - 4282
Fax     (305) 224 - 4147


                                                                           
             Peter Ehlers                                                  
             <ehlers at ucalgary.                                             
             ca>                                                        To 
                                       "Steve_Friedman at nps.gov"            
             04/01/2011 05:08          <Steve_Friedman at nps.gov>            
             PM                                                         cc 
                                       "r-help at r-project.org"              
                                       <r-help at r-project.org>              
                                                                   Subject 
                                       Re: [R] filled contour plot with    
                                       contour lines                       
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:

  for(j in 1:(varsize[4]-1)) { loop stuff }

Peter Ehlers
On 2011-04-01 11:48, Steve_Friedman at nps.gov wrote:
http://www.R-project.org/posting-guide.html
Clint Bowman
# 
Steve,

I use filled.contour but have a semicolon, ";", between the two 
axis calls.  Do you need one after

"axis(1, seq(450000 , 580000, by = 10000))"

?

Clint
David Winsemius
#
On Apr 1, 2011, at 5:38 PM, Steve_Friedman at nps.gov wrote:

            

      
      
      
    

        
That suggestion was probably intended to get you a more informative  
error message:

for(j in 1:(varsize[4]-1) )
      temp <- get.var.ncdf(
                    nc=input,
                    varid="p_foraging",
                    c(1,1,j),
                    c(varsize[1],  varsize[2], 1)
                         )

# I think Peter is correct. That loop will complete before the call to  
filled.contour,
#  so you will only have the last version of temp plot.

filled.contour(x, y, temp, color = terrain.colors,
      plot.title = title( main =
              paste("Everglades Wood Stork Foraging Potential \nYear",  
(2000+j)),

#that "double call" to title looks incomplete as well. The comma looks  
premature.
# Shouldn't it be something like:
  plot.title = bquote("Everglades Wood Stork Foraging Potential  
\nYear", .(2000+j) )

#(And since the for loop is already complete `j` will not exist.
# Which is probably the source of the error you are getting.)

             xlab = "UTM East", ylab = "UTM North") ,
             plot.axes = { contour(temp, add=T)
                axis(1, seq(450000 , 580000, by = 10000))
                axis(2, seq(2800000,4000000, by = 10000)) },
             key.title = title(main="Probability") ,
             key.axes = axis(4, seq(0 , 1 , by = 0.1))

            

      
      
      
    

        

      
      
    

        

      
      
    

        
David Winsemius, MD
West Hartford, CT

  
  


  


      

    

    

      
      

        


  

        

      Peter Ehlers
    

    

      
      #
    

  


  

      
Steve,

I was just about to send off another suggestion which
began with ...

   Try the following or wait for David W. to chime in.

But I see that he's already done that. Anyway, in case
it's still of some use:

First I would check that you don't have a variable 'T' in
your workspace. (Never use T in place of TRUE.)

Then I would check that x and y are as they should be.

Then I would make sure that temp is of the correct type
(a matrix) by letting j take a few values (1,2,varsize[4]-1),
generating temp, and running str(temp). I assume that
varsize[4] is >= 2.

Then I would run the following stripped-down version of
your loop (note that I modified your contour() call):

  for(j in 1:2) {
       temp <- get.var.ncdf(nc=input,
                 varid="p_foraging",c(1,1,j),c(varsize[1],varsize[2],1)
               )
       filled.contour(x,
                      y,
                      temp,
                      plot.axes = { contour(x, y, temp, add = TRUE)
                            axis(1, seq(450000 , 580000, by = 10000))
                            axis(2, seq(2800000,4000000, by = 10000))
                      }
  }

If that gives reasonable results, you can add the prettyfying
statements back in. If you still get errors, then either I'm
out-to-lunch (quite possible!) or you need to use debug() to
figure out what's going on.

Peter Ehlers

        
On 2011-04-01 14:59, David Winsemius wrote: