more rpy2 questions...mostly R - R-help

Erin Hodgess · 2013-11-17T23:37:28Z

An embedded and charset-unspecified text was scrubbed... Name: not available URL:

Sun, Nov 17, 2013 7:17 PM #

Erin, at first glance I would say that this is an R error.  When Rpy2
detects an error it will pass it through errors as library errors like
this.  At first glance it appears that your r code is not loading the
requisite packages as it cannot find them.  That I suspect is what is
causing your coordinates error.

I would first run R and confirm that you can load the requisite libraries
in it before depending upon them in rpy2.  In general I find that rpy2 is
a bad interface for debugging R code and you need to run it in R first to
get the problems out.

	Best,
	Collin.

On Sun, 17 Nov 2013, Erin Hodgess wrote:

Hello again!

I'm using python, rpy2, and R for a project.  It's actually pretty
interesting.  Anyhow, I pass in an R file to the python program.  However,
I am getting the following errors, which seem more like R errors(?):

Loading required package: gstat
Loading required package: automap
Error in coordinates(x.df) <- ~x + y :
  could not find function "coordinates<-"
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE,  :
  there is no package called ?gstat?
2: In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE,  :
  there is no package called ?automap?
Traceback (most recent call last):
  File "reg4.py", line 38, in <module>
    spat1.spat1(file1=file1,file2=file2)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py",
line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args,
**kwargs)
  File "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py",
line 35, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in coordinates(x.df) <- ~x + y :
  could not find function "coordinates<-"

I've checked and gstat and automap are both there.  Here is the actual R
code:
spat1 <- function(file1,file2) {
    require(gstat)
    require(automap)
    x.df <- read.table(file=file1,header=TRUE)
    coordinates(x.df) <- ~x+y
    zz <- scan(file=file2,what="character")
    proj4string(x.df) <- zz
    png(file="map1.png")
    u <- autoKrige(x.df at data[,1]~1,x.df)
    plot(u)
    return(u)
}


I know that there are a few people who have used both rpy2, python and R,
so I thought I'd launch this out.

Thanks in advance for any help.

Sincerely,
Erin


--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com

	[[alternative HTML version deleted]]