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
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