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

[Sabina Arndt]

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