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_arabica_pa.data.tmp$pa.tab_Full_GBM.img"
[2]
"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GLM.img"
[3]
"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_MARS.img"
[4]
"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_RF.img"
[5]
"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_RUN10_GBM.img"
##generate loop to create string out of the table of projected files.
L.ip = length(individual.proj)
for (i in 1:L.ip){
individual.proj.i <- individual.proj[i]
individual.proj.quote = cat(paste('"',
individual.proj.i, '"', ',',sep=""))
}
"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GBM.img","Arabica/proj_current/individual_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
email: jenny.williams@kew.org<mailto:jenny.williams@kew.org>
******************
Film: The Forgotten Home of Coffee - Beyond the
Gardens<http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw>
Stories: Coffee Expedition -
Ethiopia<http://storify.com/KewGIS/coffee-expedition-ethiopia>
Kew in Harapan Rainforest
Sumatra<http://storify.com/KewGIS/kew-in-harapan-rainforest>
Articles: Seeing the wood for the
trees<http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf>
How Kew's GIS team and South East Asia botanists are working to help
conserve and restore a rainforest in Sumatra. Download a pdf of this article
here.<http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf>
________________________________
The Royal Botanic Gardens, Kew is a non-departmental public body with exempt
charitable status, whose principal place of business is at Royal Botanic
Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.
The information contained in this email and any attachments is intended solely
for the addressee(s) and may contain confidential or legally privileged
information. If you have received this message in error, please return it
immediately and permanently delete it. Do not use, copy or disclose the
information contained in this email or in any attachment.
Any views expressed in this email do not necessarily reflect the opinions of RBG
Kew.
Any files attached to this email have been inspected with virus detection
software by RBG Kew before transmission, however you should carry out your own
virus checks before opening any attachments. RBG Kew accepts no liability for
any loss or damage which may be caused by software viruses.
[[alternative HTML version deleted]]
Hi Jenny, Firstly, to my knowledge you cannot assign the output of cat to an object (i.e. it only prints it). Second, you can just add the 'collapse' option of the paste function. individual.proj.quote <- paste(individual.proj, collapse = ",") if you really want the quotes individual.proj.quote <- paste(individual.proj, collapse='","') but you will be stuck with some backslashes I can't recall the syntax to remove. Hope this serves your purposes Cheers, Charles On Thu, Aug 8, 2013 at 10:05 AM, Jenny Williams <jenny.williams@kew.org>wrote:> 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_arabica_pa.data.tmp$pa.tab_Full_GBM.img" > [2] > "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GLM.img" > [3] > "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_MARS.img" > [4] > "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_RF.img" > [5] > "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_RUN10_GBM.img" > > > ##generate loop to create string out of the table of projected files. > L.ip = length(individual.proj) > for (i in 1:L.ip){ > individual.proj.i <- individual.proj[i] > individual.proj.quote = cat(paste('"', individual.proj.i, '"', > ',',sep="")) > } > > "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GBM.img","Arabica/proj_current/individual_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 > email: jenny.williams@kew.org<mailto:jenny.williams@kew.org> > ****************** > > Film: The Forgotten Home of Coffee - Beyond the Gardens< > http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw> > Stories: Coffee Expedition - Ethiopia< > http://storify.com/KewGIS/coffee-expedition-ethiopia> > Kew in Harapan Rainforest Sumatra< > http://storify.com/KewGIS/kew-in-harapan-rainforest> > Articles: Seeing the wood for the trees< > http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf > > > How Kew's GIS team and South East Asia botanists are working to help > conserve and restore a rainforest in Sumatra. Download a pdf of this > article here.< > http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf > > > > > ________________________________ > The Royal Botanic Gardens, Kew is a non-departmental public body with > exempt charitable status, whose principal place of business is at Royal > Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. > > The information contained in this email and any attachments is intended > solely for the addressee(s) and may contain confidential or legally > privileged information. If you have received this message in error, please > return it immediately and permanently delete it. Do not use, copy or > disclose the information contained in this email or in any attachment. > > Any views expressed in this email do not necessarily reflect the opinions > of RBG Kew. > > Any files attached to this email have been inspected with virus detection > software by RBG Kew before transmission, however you should carry out your > own virus checks before opening any attachments. RBG Kew accepts no > liability for any loss or damage which may be caused by software viruses. > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@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. >-- Charles Determan Integrated Biosciences PhD Candidate University of Minnesota [[alternative HTML version deleted]]
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
email: jenny.williams at kew.org<mailto:jenny.williams at kew.org>
******************
Film: The Forgotten Home of Coffee - Beyond the
Gardens<http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw>
Stories: Coffee Expedition -
Ethiopia<http://storify.com/KewGIS/coffee-expedition-ethiopia>
Kew in Harapan Rainforest
Sumatra<http://storify.com/KewGIS/kew-in-harapan-rainforest>
Articles: Seeing the wood for the
trees<http://www.kew.org/ucm/groups/public/documents/document/kp
pcont_060602.pdf>
How Kew's GIS team and South East Asia botanists are working to
help conserve and restore a rainforest in Sumatra. Download a
pdf of this article
here.<http://www.kew.org/ucm/groups/public/documents/document/kp
pcont_060602.pdf>
________________________________
The Royal Botanic Gardens, Kew is a non-departmental public body
with exempt charitable status, whose principal place of business
is at Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB,
United Kingdom.
The information contained in this email and any attachments is
intended solely for the addressee(s) and may contain
confidential or legally privileged information. If you have
received this message in error, please return it immediately and
permanently delete it. Do not use, copy or disclose the
information contained in this email or in any attachment.
Any views expressed in this email do not necessarily reflect the
opinions of RBG Kew.
Any files attached to this email have been inspected with virus
detection software by RBG Kew before transmission, however you
should carry out your own virus checks before opening any
attachments. RBG Kew accepts no liability for any loss or damage
which may be caused by software viruses.
[[alternative HTML version deleted]]
______________________________________________
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.
On Thu, Aug 08, 2013 at 04:05:57PM +0100, Jenny Williams wrote:> 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: NULLThis is a somewhat frequent confusion of the (very different!) concepts of assignment and printing. The fact that something becomes visible to the human user via printing has nothing to do really with the fact that an object is generated and assigned to a variable, thereby becoming accessible (and, in that allegorical sense, "visible") to the subsequent code. The cat function prints values but it does not return them. It returns NULL, which is what you get.> individual.proj = Sys.glob("Arabica/proj_current/individual_projections/*.img", dirmark = FALSE) > individual.proj > [1] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GBM.img" > [2] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GLM.img" > [3] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_MARS.img" > [4] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_RF.img" > [5] "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_RUN10_GBM.img" > > > ##generate loop to create string out of the table of projected files. > L.ip = length(individual.proj) > for (i in 1:L.ip){ > individual.proj.i <- individual.proj[i] > individual.proj.quote = cat(paste('"', individual.proj.i, '"', ',',sep="")) > } > "Arabica/proj_current/individual_projections/proj_current_arabica_pa.data.tmp$pa.tab_Full_GBM.img","Arabica/proj_current/individual_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.If you don't mind me suggesting this, reading the documentation page of the function(s) you use is an approach that is more targeted and therefore often quicker. (Googling "cat" is probably especially bad, as there are various cat applications and functions in several languages, not to mention several species of mammals... ;-) ) As a further remark, you don't need a loop, one line composed of sprintf and paste (check the collapse parameter) should do the trick you're after. Best regards, Jan> > ****************** > 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 > email: jenny.williams at kew.org<mailto:jenny.williams at kew.org> > ****************** > > Film: The Forgotten Home of Coffee - Beyond the Gardens<http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw> > Stories: Coffee Expedition - Ethiopia<http://storify.com/KewGIS/coffee-expedition-ethiopia> > Kew in Harapan Rainforest Sumatra<http://storify.com/KewGIS/kew-in-harapan-rainforest> > Articles: Seeing the wood for the trees<http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf> > How Kew's GIS team and South East Asia botanists are working to help conserve and restore a rainforest in Sumatra. Download a pdf of this article here.<http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf> > > > ________________________________ > The Royal Botanic Gardens, Kew is a non-departmental public body with exempt charitable status, whose principal place of business is at Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. > > The information contained in this email and any attachments is intended solely for the addressee(s) and may contain confidential or legally privileged information. If you have received this message in error, please return it immediately and permanently delete it. Do not use, copy or disclose the information contained in this email or in any attachment. > > Any views expressed in this email do not necessarily reflect the opinions of RBG Kew. > > Any files attached to this email have been inspected with virus detection software by RBG Kew before transmission, however you should carry out your own virus checks before opening any attachments. RBG Kew accepts no liability for any loss or damage which may be caused by software viruses. > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.-- +- Jan T. Kim -------------------------------------------------------+ | email: jttkim at gmail.com | | WWW: http://www.jtkim.dreamhosters.com/ | *-----=< hierarchical systems are for files, not for humans >=-----*
If I understand the request correctly, here is an easy to follow example: (I'm using the first four letters as surrogates for the file names) (and assuming we want quotes at both the beginning and the end)> tmp <- letters[1:4] > tmp[1] "a" "b" "c" "d"> foo <- paste( "'", paste(tmp,collapse="','"), "'", sep='') > cat(foo,'\n')'a','b','c','d' In this case, cat() does a better job than print() of telling you exactly what you have. I use this sort of thing to construct arguments for the SQL "in" clause) -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 8/8/13 8:05 AM, "Jenny Williams" <jenny.williams at kew.org> wrote:>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_arabica_pa.data. >tmp$pa.tab_Full_GBM.img" > [2] >"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data. >tmp$pa.tab_Full_GLM.img" > [3] >"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data. >tmp$pa.tab_Full_MARS.img" > [4] >"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data. >tmp$pa.tab_Full_RF.img" > [5] >"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data. >tmp$pa.tab_RUN10_GBM.img" > > >##generate loop to create string out of the table of projected files. >L.ip = length(individual.proj) > for (i in 1:L.ip){ > individual.proj.i <- individual.proj[i] > individual.proj.quote = cat(paste('"', individual.proj.i, '"', >',',sep="")) > } >"Arabica/proj_current/individual_projections/proj_current_arabica_pa.data. >tmp$pa.tab_Full_GBM.img","Arabica/proj_current/individual_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 >email: jenny.williams at kew.org<mailto:jenny.williams at kew.org> >****************** > >Film: The Forgotten Home of Coffee - Beyond the >Gardens<http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw> >Stories: Coffee Expedition - >Ethiopia<http://storify.com/KewGIS/coffee-expedition-ethiopia> > Kew in Harapan Rainforest >Sumatra<http://storify.com/KewGIS/kew-in-harapan-rainforest> >Articles: Seeing the wood for the >trees<http://www.kew.org/ucm/groups/public/documents/document/kppcont_0606 >02.pdf> >How Kew's GIS team and South East Asia botanists are working to help >conserve and restore a rainforest in Sumatra. Download a pdf of this >article >here.<http://www.kew.org/ucm/groups/public/documents/document/kppcont_0606 >02.pdf> > > >________________________________ >The Royal Botanic Gardens, Kew is a non-departmental public body with >exempt charitable status, whose principal place of business is at Royal >Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. > >The information contained in this email and any attachments is intended >solely for the addressee(s) and may contain confidential or legally >privileged information. If you have received this message in error, >please return it immediately and permanently delete it. Do not use, copy >or disclose the information contained in this email or in any attachment. > >Any views expressed in this email do not necessarily reflect the opinions >of RBG Kew. > >Any files attached to this email have been inspected with virus detection >software by RBG Kew before transmission, however you should carry out >your own virus checks before opening any attachments. RBG Kew accepts no >liability for any loss or damage which may be caused by software viruses. > > [[alternative HTML version deleted]] > >______________________________________________ >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.