How to remove square brackets, etc. from address strings?

Sun, May 27, 2012 2:12 PM

Hello r-help members,

thank you very much for your reply, Rui Barradas.

Unfortunately, I'm not sure if I understand it correctly: I don't know 
how to create the vector's second element y that way. The pattern you 
used has to be extracted from the address strings first. This is more 
complex as I'd tried to explain in my previous posts. It finally seems 
to work now.

Do you happen to have any idea on how I could put the country names back 
into their original lines / order, though?

Thank you very much in advance!
Faithfully yours,

Sabina Arndt


Am 27.05.2012 19:04, schrieb Rui Barradas:

Hello,

Though I've not been following this thread, it seems like a regular 
expressions problem.
In the code below, I've created a 'testdata' variable based on your post.

# create a vector with two elements.
x <- "[Engel, Kathrin M. Y.; Schroeck, ... etc ...
y <- gsub("Germany", "Portugal", x)
testdata <- c(x, y)

# 's' is a list of character vectors, each element's final word is a 
country
s <- strsplit(testdata, ";[[:space:]]+\\[")
lapply(s, function(x) sapply(strsplit(x, "[[:blank:]]"), tail, 1))


If this isn't it, sorry for the intrusion.

Rui Barradas

Em 27-05-2012 17:29, Sabina Arndt escreveu:

Hello r-help members,

I'm very grateful for the reply which Sarah Goslee sent to me in such 
a prompt and helpful manner.
It took me some time, but with a few amendments her suggestion now 
works not only for an example but for my entire data file as well:

results

  [1] "GERMANY"         "GERMANY"         "GERMANY"        "GERMANY"
  [5] "GERMANY"         "GERMANY"         "GERMANY"        "GERMANY"
...

Thank you very much for that, dear Sarah!

All these names actually belong to the very first record, though, 
which contains eight addresses instead of only one:

testdata[1]

  [1] "[Engel, Kathrin M. Y.; Schroeck, Kristin; Schoeneberg, 
Torsten; Schulz, Angela] Univ Leipzig, Fac Med, Inst Biochem, 
Leipzig, Germany; [Teupser, Daniel; Holdt, Lesca Miriam; Thiery, 
Joachim] Univ Leipzig, Fac Med, Inst Lab Med Clin Chem & Mol 
Diagnost, Leipzig, Germany; [Toenjes, Anke; Kern, Matthias; Blueher, 
Matthias; Stumvoll, Michael] Univ Leipzig, Fac Med, Dept Internal 
Med, Leipzig, Germany; [Dietrich, Kerstin; Kovacs, Peter] Univ 
Leipzig, Fac Med, Interdisciplinary Ctr Clin Res, Leipzig, Germany; 
[Kruegel, Ute] Univ Leipzig, Fac Med, Rudolf Boehm Inst Pharmacol & 
Toxicol, Leipzig, Germany; [Scheidt, Holger A.; Schiller, Juergen; 
Huster, Daniel] Univ Leipzig, Fac Med, Inst Med Phys & Biophys, 
Leipzig, Germany; [Brockmann, Gudrun A.] Humboldt Univ, Inst Anim 
Sci, D-10099 Berlin, Germany; [Augustin, Martin] Ingenium Pharmaceut 
AG, Martinsried, Germany"

results[1]

  [1] "GERMANY"

How can I put the country names back into their original lines / order?
This is an example of the correct result I'd like to receive:

results[1]

  [1] "GERMANY" "GERMANY" "GERMANY" "GERMANY" "GERMANY" "GERMANY" 
"GERMANY" "GERMANY"

How can I achieve this result?

I think counting the semicolons outside square brackets - i.e. the 
ones before a "[" but behind a "]" would be helpful in this regard, 
but I'm not sure how to do that, unfortunately. These semicolons 
directly follow the country names, like this, e.g.: "... Germany; [..."
If I add "+ 1" to their number it results in the number of addresses 
for each record / line.

Thank you very much in advance!

Faithfully yours,

Sabina Arndt


Am 26.05.2012 00:19, schrieb Sarah Goslee:

Part of your problem is that your regexes have spaces in them, so
that's what you're matching.

A small reproducible example would be more useful. I'm not feeling
inclined to wade through all your linked files on Friday evening, but
see if this helps:

testdata<- "[Engel, Kathrin M. Y.; Schroeck, Kristin; Schoeneberg, 
Torsten; Schulz, Angela] Univ Leipzig, Fac Med, Inst Biochem, 
Leipzig, New Zealand; [Teupser, Daniel; Holdt, Lesca Miriam; 
Thiery, Joachim] Univ Leipzig, Fac Med, Inst Lab Med Clin Chem&  
Mol Diagnost, Leipzig, USA; [Toenjes, Anke; Kern, Matthias; 
Blueher, Matthias; Stumvoll, Michael] Univ Leipzig, Fac Med, Dept 
Internal Med, Leipzig, Germany; [Dietrich, Kerstin; Kovacs, Peter] 
Univ Leipzig, Fac Med, Interdisciplinary Ctr Clin Res, Leipzig, 
Germany; [Kruegel, Ute] Univ Leipzig, Fac Med, Rudolf Boehm Inst 
Pharmacol&  Toxicol, Leipzig, Germany; [Scheidt, Holger A.; 
Schiller, Juergen; Huster, Daniel] Univ Leipzig, Fac Med, Inst Med 
Phys&  Biophys, Leipzig, Germany; [Brockmann, Gudrun A.] Humboldt 
Univ, Inst Anim Sci, D-10099 Berlin, Germany; [Augustin, Martin] 
Ingenium Pharmaceut AG, Martinsried, Germany"
results<- gsub("\\[.*?\\]", "", testdata)
results<- unlist(strsplit(results, ";"))
results<- sapply(results, function(x)sub("^.*, ([A-Za-z ]*)$", 
"\\1", x))
names(results)<- NULL
results

[1] "New Zealand" "USA"         "Germany"     "Germany"     "Germany"
    "Germany"     "Germany"     "Germany"


Sarah

On Fri, May 25, 2012 at 4:31 PM, Sabina 
Arndt<sabina.arndt at hotmail.de>  wrote:

Hello r-help members,

the solutions which Sarah Goslee and arun sent to me in such a 
prompt and
helpful manner work well with the examples I cut from the 
data.frame I'm
analyzing. Thank you very much for that!
I incorporated them into my R-script and discovered that it still 
doesn't
work properly, unfortunately. I have no idea why that's the case.
You see, I want to extract country names from the contents of 
tab-delimited
text files. This is an example of the data I'm using:
http://pastebin.com/mYZNDXg6
This is the script I'm using to import the data:
http://pastebin.com/Z10UUH3z (It requires the text files to be in a 
folder
which doesn't contain any other .txt files.)
This is the script I'm using to extract the country names:
http://pastebin.com/G37fuPba
This is the string that's in the relevant field of the first record 
I'm
working on:

[Engel, Kathrin M. Y.; Schroeck, Kristin; Schoeneberg, Torsten; 
Schulz,
Angela] Univ Leipzig, Fac Med, Inst Biochem, Leipzig, Germany; 
[Teupser,
Daniel; Holdt, Lesca Miriam; Thiery, Joachim] Univ Leipzig, Fac 
Med, Inst
Lab Med Clin Chem&  Mol Diagnost, Leipzig, Germany; [Toenjes, Anke; 
Kern,
Matthias; Blueher, Matthias; Stumvoll, Michael] Univ Leipzig, Fac 
Med, Dept
Internal Med, Leipzig, Germany; [Dietrich, Kerstin; Kovacs, Peter] 
Univ
Leipzig, Fac Med, Interdisciplinary Ctr Clin Res, Leipzig, Germany;
[Kruegel, Ute] Univ Leipzig, Fac Med, Rudolf Boehm Inst Pharmacol&  
Toxicol,
Leipzig, Germany; [Scheidt, Holger A.; Schiller, Juergen; Huster, 
Daniel]
Univ Leipzig, Fac Med, Inst Med Phys&  Biophys, Leipzig, Germany;
[Brockmann, Gudrun A.] Humboldt Univ, Inst Anim Sci, D-10099 Berlin,
Germany; [Augustin, Martin] Ingenium Pharmaceut AG, Martinsried, 
Germany

This is the incorrect result my extraction script gives me for the 
first
record:

C1s[1]

  [1] "[ENGEL,  KATHRIN M. Y." "KRISTIN"                "TORSTEN"
  [4] "GERMANY"                "DANIEL"                 "LESCA MIRIAM"
  [7] "GERMANY"                "ANKE"                   "MATTHIAS"
[10] "MATTHIAS"               "GERMANY"                "KERSTIN"
[13] "GERMANY"                "GERMANY"                "[SCHEIDT,  
HOLGER
A."
[16] "JUERGEN"                "GERMANY"                "HUMBOLDT"
[19] "GERMANY"

For some reason the first and sixth pair of the eight square 
brackets are
not removed ... Do you understand why?
Instead I'd like to get this result, though:

C1s[1]

  [1] "GERMANY"        "GERMANY"        "GERMANY"
  [4] "GERMANY"        "GERMANY"        "GERMANY"
  [7] "HUMBOLDT"        "GERMANY"

What am I doing wrong? What are the errors in my R-script?
Would anybody be so kind as to take a look and help me out, please?
Thank you very much in advance!

Faithfully yours,

Sabina Arndt

How to remove square brackets, etc. from address strings?

Thread (12 messages)