Hello,
I am running R under Ubuntu 8.04. I am trying to do numerous linear
fits to various subsets of my data set. I am having trouble convincing
R to send the output from these fits to text files from within a script.
When I run my script, all the plots are created as postscript files in
the correct directory, and text files appear with the correct names for
all the summaries of the fits. However, all of these files are blank!
If I copy/paste the "sink" commands from my script manually into the
command line, the files are created correctly, but if the same commands
are executed from within my script, no output is generated.
The output section of my script, which correctly creates the plots I
want, but not the text, is:
x_seq1_fit=lm(xagb$X5mag[x_seq1_filt]~x1per)
x_seq2_fit=lm(xagb$X5mag[x_seq2_filt]~x2per)
setwd("/home/driebel/sage/output/pl_fits/R/5mag/chem")
postscript(file="x_seq1_fit.ps")
plot(x1per,xagb$X5mag[x_seq1_filt],ylim=c(13,7))
abline(x_seq1_fit,col="red")
dev.off()
postscript(file="x_seq1_resid.ps")
plot(x1per,x_seq1_fit$res)
abline(h=0,col="red")
dev.off()
postscript(file="x_seq2_fit.ps")
plot(x2per,xagb$X5mag[x_seq2_filt],ylim=c(13,7))
abline(x_seq2_fit,col="red")
dev.off()
postscript(file="x_seq2_resid.ps")
plot(x2per,x_seq2_fit$res)
abline(h=0,col="red")
dev.off()
sink(file="x_seq2_fit.dat")
summary(x_seq2_fit)
sink()
sink(file="x_seq1_fit.dat")
summary(x_seq1_fit)
sink()
Is there something else one must do with "sink" from within a script?
Thanks for your help,
Dave
running a .r script and saving the output to a file
4 messages · David Riebel, Sarah Goslee, jim holtman +1 more
Hi Dave, I don't know about using sink(), but if you run your script in batch mode all the output will be saved to a text file foryou. R CMD BATCH infile outfile (at the linux prompt, not from within R). Sarah
On Sun, Jul 26, 2009 at 4:47 PM, David Riebel<driebel at pha.jhu.edu> wrote:
Hello,
I am running R under Ubuntu 8.04. ?I am trying to do numerous linear
fits to various subsets of my data set. ?I am having trouble convincing
R to send the output from these fits to text files from within a script.
When I run my script, all the plots are created as postscript files in
the correct directory, and text files appear with the correct names for
all the summaries of the fits. ?However, all of these files are blank!
If I copy/paste the "sink" commands from my script manually into the
command line, the files are created correctly, but if the same commands
are executed from within my script, no output is generated.
The output section of my script, which correctly creates the plots I
want, but not the text, is:
x_seq1_fit=lm(xagb$X5mag[x_seq1_filt]~x1per)
x_seq2_fit=lm(xagb$X5mag[x_seq2_filt]~x2per)
setwd("/home/driebel/sage/output/pl_fits/R/5mag/chem")
postscript(file="x_seq1_fit.ps")
plot(x1per,xagb$X5mag[x_seq1_filt],ylim=c(13,7))
abline(x_seq1_fit,col="red")
dev.off()
postscript(file="x_seq1_resid.ps")
plot(x1per,x_seq1_fit$res)
abline(h=0,col="red")
dev.off()
postscript(file="x_seq2_fit.ps")
plot(x2per,xagb$X5mag[x_seq2_filt],ylim=c(13,7))
abline(x_seq2_fit,col="red")
dev.off()
postscript(file="x_seq2_resid.ps")
plot(x2per,x_seq2_fit$res)
abline(h=0,col="red")
dev.off()
sink(file="x_seq2_fit.dat")
summary(x_seq2_fit)
sink()
sink(file="x_seq1_fit.dat")
summary(x_seq1_fit)
sink()
Is there something else one must do with "sink" from within a script?
Thanks for your help,
Dave
Sarah Goslee http://www.functionaldiversity.org
You have to explicitly 'print' the output. At the command line there is an implicit 'print'. Try: sink(file="x_seq2_fit.dat") print(summary(x_seq2_fit)) sink() sink(file="x_seq1_fit.dat") print(summary(x_seq1_fit)) sink()
On Sun, Jul 26, 2009 at 4:47 PM, David Riebel<driebel at pha.jhu.edu> wrote:
Hello,
I am running R under Ubuntu 8.04. ?I am trying to do numerous linear
fits to various subsets of my data set. ?I am having trouble convincing
R to send the output from these fits to text files from within a script.
When I run my script, all the plots are created as postscript files in
the correct directory, and text files appear with the correct names for
all the summaries of the fits. ?However, all of these files are blank!
If I copy/paste the "sink" commands from my script manually into the
command line, the files are created correctly, but if the same commands
are executed from within my script, no output is generated.
The output section of my script, which correctly creates the plots I
want, but not the text, is:
x_seq1_fit=lm(xagb$X5mag[x_seq1_filt]~x1per)
x_seq2_fit=lm(xagb$X5mag[x_seq2_filt]~x2per)
setwd("/home/driebel/sage/output/pl_fits/R/5mag/chem")
postscript(file="x_seq1_fit.ps")
plot(x1per,xagb$X5mag[x_seq1_filt],ylim=c(13,7))
abline(x_seq1_fit,col="red")
dev.off()
postscript(file="x_seq1_resid.ps")
plot(x1per,x_seq1_fit$res)
abline(h=0,col="red")
dev.off()
postscript(file="x_seq2_fit.ps")
plot(x2per,xagb$X5mag[x_seq2_filt],ylim=c(13,7))
abline(x_seq2_fit,col="red")
dev.off()
postscript(file="x_seq2_resid.ps")
plot(x2per,x_seq2_fit$res)
abline(h=0,col="red")
dev.off()
sink(file="x_seq2_fit.dat")
summary(x_seq2_fit)
sink()
sink(file="x_seq1_fit.dat")
summary(x_seq1_fit)
sink()
Is there something else one must do with "sink" from within a script?
Thanks for your help,
Dave
______________________________________________ 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.
Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve?
Check out: http://akastrin.wordpress.com/category/r/
David Riebel wrote:
Hello,
I am running R under Ubuntu 8.04. I am trying to do numerous linear
fits to various subsets of my data set. I am having trouble convincing
R to send the output from these fits to text files from within a script.
When I run my script, all the plots are created as postscript files in
the correct directory, and text files appear with the correct names for
all the summaries of the fits. However, all of these files are blank!
If I copy/paste the "sink" commands from my script manually into the
command line, the files are created correctly, but if the same commands
are executed from within my script, no output is generated.
The output section of my script, which correctly creates the plots I
want, but not the text, is:
x_seq1_fit=lm(xagb$X5mag[x_seq1_filt]~x1per)
x_seq2_fit=lm(xagb$X5mag[x_seq2_filt]~x2per)
setwd("/home/driebel/sage/output/pl_fits/R/5mag/chem")
postscript(file="x_seq1_fit.ps")
plot(x1per,xagb$X5mag[x_seq1_filt],ylim=c(13,7))
abline(x_seq1_fit,col="red")
dev.off()
postscript(file="x_seq1_resid.ps")
plot(x1per,x_seq1_fit$res)
abline(h=0,col="red")
dev.off()
postscript(file="x_seq2_fit.ps")
plot(x2per,xagb$X5mag[x_seq2_filt],ylim=c(13,7))
abline(x_seq2_fit,col="red")
dev.off()
postscript(file="x_seq2_resid.ps")
plot(x2per,x_seq2_fit$res)
abline(h=0,col="red")
dev.off()
sink(file="x_seq2_fit.dat")
summary(x_seq2_fit)
sink()
sink(file="x_seq1_fit.dat")
summary(x_seq1_fit)
sink()
Is there something else one must do with "sink" from within a script?
Thanks for your help,
Dave