[R] For loop output

Fri Aug 9 13:33:44 CEST 2013

To update on the use of this little string, I am trying to use it to automate files to be loaded into a raster stack.
I think the issue I have with the string is related to the backslashes. I need to just read the pure text so that the datasets can be sourced, though I am not sure whether the stack function will accept a string of files in this format either!

>individual.proj.quote <-capture.output(write.table(matrix(individual.proj, 1), quote=TRUE, sep=",", row.names=FALSE, col.names=FALSE))

> individual.proj.quote
[1] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GBM.img\",\"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GLM.img\",\"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_MARS.img\",\"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_RF.img" 

>test4 = stack(individual.proj.quote)
Cannot create a RasterLayer object from this file. (file does not exist)

I ran a test with just one file which worked, but haven't managed to combine more files into the stack:

>test
[1] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GBM.img"

> library(raster)
> test.1 = stack(test)
> test.1
class       : RasterStack 
dimensions  : 9241, 8521, 78742561, 1  (nrow, ncol, ncell, nlayers)
resolution  : 0.008333334, 0.008333334  (x, y)
extent      : -18.00832, 53.00001, -38.00833, 39.00001  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +ellps=WGS84 +no_defs 
names       : proj_current_arabica_pa.data.tmp.pa.tab_Full_GBM 
min values  :                                                6 
max values  :                                              995

-----Original Message-----
From: David Carlson [mailto:dcarlson at tamu.edu] 
Sent: 08 August 2013 18:04
To: Jenny Williams; r-help at r-project.org
Subject: RE: [R] For loop output

It's not clear how you are planning to use this within R, but you don't need a loop.

individual.proj.quote <-
capture.output(write.table(matrix(individual.proj, 1), quote=TRUE, sep=",", row.names=FALSE, col.names=FALSE))

This produces a single character string which consists of the quoted file names separated by commas.

-------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77840-4352

-----Original Message-----
From: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of Jenny Williams
Sent: Thursday, August 8, 2013 10:06 AM
To: 'r-help at r-project.org'
Subject: [R] For loop output

I am having difficulty storing the output of a for loop I have generated. All I want to do is find all the files that I have, create a string with all of the names in quotes and separated by commas. This is proving more difficult than I initially anticipated.
I am sure it is either very simple or the construction of the for loop is not quite right The result gets automatically printed after the loop but I can't seem to save it.
I have tried to create the element in advance but the result is the same: NULL

individual.proj =
Sys.glob("Arabica/proj_current/individual_projections/*.img",
dirmark = FALSE)
individual.proj
[1]
"Arabica/proj_current/individual_projections/proj_current_arabic
a_pa.data.tmp$pa.tab_Full_GBM.img"
 [2]
"Arabica/proj_current/individual_projections/proj_current_arabic
a_pa.data.tmp$pa.tab_Full_GLM.img"
 [3]
"Arabica/proj_current/individual_projections/proj_current_arabic
a_pa.data.tmp$pa.tab_Full_MARS.img"
 [4]
"Arabica/proj_current/individual_projections/proj_current_arabic
a_pa.data.tmp$pa.tab_Full_RF.img"
 [5]
"Arabica/proj_current/individual_projections/proj_current_arabic
a_pa.data.tmp$pa.tab_RUN10_GBM.img"

##generate loop to create string out of the table of projected files.
L.ip = length(individual.proj)
  for (i in 1:L.ip){
           individual.proj.i <- individual.proj[i]
           individual.proj.quote = cat(paste('"', individual.proj.i, '"', ',',sep=""))
           }
"Arabica/proj_current/individual_projections/proj_current_arabic
a_pa.data.tmp$pa.tab_Full_GBM.img","Arabica/proj_current/individ
ual_projections/proj_current....

##print output string
individual.proj.quote
NULL

#command to be applied to individual.proj.quote to removed the final comma from the string substr(individual.proj.quote, 1, nchar(individual.proj.quote)-1)

Any help or pointers would be greatly appreciated, no amount of extensive google searches have been fruitful so far.

******************
Jenny Williams
Spatial Information Scientist, GIS Unit
Herbarium, Library, Art & Archives Directorate Royal Botanic Gardens, Kew Richmond, TW9 3AB, UK

Tel: +44 (0)208 332 5277
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