Help integrating R code into Perl code

kantica has asked for the wisdom of the Perl Monks concerning the following question:

Hello everyone! I am a student and I am learning Perl. For my project I am writing a script whose output is a .csv file and I would like to call an R script from the Perl script so I could show the results from my .csv in a graph. I have a code which works in R:

setwd("C://PerlProject")
# loading data into R
indata <- read.table ("result.csv", colClasses=c(NA,"NULL","NULL",NA,N
+A,NA,NA,NA,NA), header = TRUE, sep = ",")

# load the stats package
library(stats)
mydata <- indata[,2:8]
ir_pca <- prcomp(mydata,
                 center = TRUE,
                 scale. = TRUE)

scrs <-ir_pca$x[, 1:2]
pdf("plots.pdf", width=16, height=16)
plot(scrs)
text( scrs, rownames( indata ), pos= 3 )
dev.off()
[download]

but I am having real troubles integrating it in my Perl script. I've instaled the Statistics::R package, but when I tried to put these commands in the $R <- run () way, I just get a bunch of errors. Could anyone at least give me some tips how to go around it? Thank you so much! p.s. The file 'result.csv' is a variable $result in Perl, I am not sure how to connect these too?

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Re: Help integrating R code into Perl code by poj (Abbot) on Jun 18, 2016 at 15:31 UTC
See Calling R in perl. If you have a working R script then you should be able to use `#!perl use strict; use Statistics::R; my $R = Statistics::R->new(); $R->run_from_file( 'c:/folder/myprogram.R' );` [download] poj	[reply] [d/l]
Re^2: Help integrating R code into Perl code by kantica (Initiate) on Jun 18, 2016 at 18:28 UTC
Thank you so much! After I've updated the Win32API::File this worked, although I still have two warnings which I am trying to work out: "Warning: unable to close filehandle GEN25 properly: Bad file descriptor at C:/Strawberry/perl/vendor/lib/IPC/Run/Win32IO.pm line 126."	[reply]
Re^3: Help integrating R code into Perl code by Yary (Pilgrim) on Jun 19, 2016 at 15:13 UTC
A few things to try any-or-all-of: Since this is a warning from a library you didn't write, you can silence warnings from it by enclosing it in a block and turning off warnings in the dynamic scope. { local $^W = 0; call_library_that_warns(); } Make a very small example that warns- perhaps running a "Hello World" R script- and post a bug report. It could be a bug in either Statistics::R or Win32API::File - but since the example would start with R, then I'd start by reporting there. If you're ambitious and have time, run that small example script in the debugger shell "`perl -d Hello_World_r.pl`", and try to find out more about the problem, and perhaps create a patch you can send to the appropriate party...	[reply]
Re^4: Help integrating R code into Perl code by AnomalousMonk (Archbishop) on Jun 19, 2016 at 22:22 UTC
Re: Help integrating R code into Perl code by Anonymous Monk on Jun 18, 2016 at 13:51 UTC
How do I post a question effectively? What is "a bunch of errors" and what does the Perl code that produces them look like?	[reply]
Re: Help integrating R code into Perl code by perlfan (Parson) on Jun 22, 2016 at 13:17 UTC
I saw this a while back. It's uses Statistics::R and Data::Frame.	[reply]