Out of memory issue

On Apr 24, 2009, at 9:06 PM, Neotropical bat risk assessments wrote:

 Hi all,
 Julian just reminded me I need to include the lines of code so  
here it is
 below.
 I am trying to run some plots on data, but when loading the CSV  
data file it
 doss that but in ggplot R is stopping and I am getting an out of  
memory
 error.

d <- read.csv batcalls.rda

 Error: unexpected symbol in "d <- read.csv batcalls.rda"

If you really do have a data file called batcalls.rda, then the  
proper way to get it into memory is with:

load("C:/Rainey//batcalls.rda")  # replace path with the actual path  
on your system and remember not to use "\"'s

attach(d)

 Error in attach(d) : object "d" not found

Because of the error ... nothing got done.

library(ggplot2)
print(qplot(Sc, Fc))

 Error in eval(expr, envir, enclos) : object "Sc" not found

You cannot do anything on something that isn't there

data(batcalls)
  attach(batcalls)
  print(qplot(Fc,geom="density"))
  b<-kmeans(Fc,c(10,15,18,30))
 print(qplot(Sc,Fc,colour=as.factor(b$cluster)))

print(qplot(Dur,geom="density"))
  b<-kmeans(Dur,c(10,15,18,30))
 print(qplot(Dur,Fc,colour=as.factor(b$cluster)))

d <- read.csv ("C:/Rainey/RainyAllbats.csv")

OK, that appears to have run without error, so it fits into memory.  
Now you should run:
str(d)   # and report the results

attach(d)

        The following object(s) are masked from batcalls :
         Dc Dur Fc Fk Fmax Fmean Fmin Qk Qual S1 Sc st TBC Tc Tk

library(ggplot2)
print(qplot(Sc, Fc))

 Warning messages:
 1: In data.frame(..., check.names = FALSE) :
   Reached total allocation of 1535Mb: see help(memory.size)
 2: In data.frame(..., check.names = FALSE) :
   Reached total allocation of 1535Mb: see help(memory.size)
 3: Removed 1200249 rows containing missing values (geom_point).

data(d)

 Warning message:
 In data(d) : data set 'd' not found

  attach(d)

        The following object(s) are masked from d ( position 3 ) :
         Dc Dur Fc Filename Fk Fmax Fmean Fmin Qk Qual S1 Sc st TBC  
Tc Tk
        The following object(s) are masked from batcalls :
         Dc Dur Fc Fk Fmax Fmean Fmin Qk Qual S1 Sc st TBC Tc Tk

  print(qplot(Fc,geom="density"))

 There were 15 warnings (use warnings() to see them)

  b<-kmeans(Fc,c(10,15,18,30))

 Error in switch(nmeth, { : NA/NaN/Inf in foreign function call  
(arg 1)

f=jpeg(file="Sc x Fc.jpg")
 print(qplot(Sc,Fc,colour=as.factor(b$cluster)))

 Error in data.frame(colour = c(3L, 4L, 4L, 4L, 4L, 1L, 4L, 2L, 1L,  
1L, :
   arguments imply differing number of rows: 9404, 2400489

You seem to be ignoring all the informative error message.

dev.off()

 Anyway to tweak this somehow to get it to run?
 Using WinXP with 4 GB RAM

WinXP in its default state can only use around 2.5GB and that may  
require upping the memory limits:
<http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021 

And read the material in the links from that page as well.

-- 


David Winsemius, MD
Heritage Laboratories
West Hartford, CT