Re: [R] Relist strings? [Was: How to remove square brackets, etc. from address strings?]

Rui Barradas Tue, 29 May 2012 05:03:00 -0700

Hello,

The error message means that 'x' is not a character vector. Can't youtry it only with the text in the link you've posted,http://pastebin.com/mYZNDXg6 ?


I'm asking this because I've just checked it and it doesn't give any eror.

Em 29-05-2012 12:39, Sabina Arndt escreveu:

Hello r-help members,

thank you very much for your reply, Rui Barradas.

Your data file has more than one line.

Yes, each line is a new record and I read several such data files into one 
data.frame.

This is problably why it gives you that error. Process just one file,like I've said, then say something.(Moreover, it makes sense to solve the problems with a smaller set thenmove on to the larger one.)


Rui Barradas

I've called it "sabrina.txt" and then processed with:

x<- readLines("sabrina.txt")

s<- strsplit(x, ";[[:space:]]\\[")

Thank you; but this gives me an error message:

Error in strsplit(x, ";[[:space:]]\\[") : non-character argument

So I cannot check the rest of your suggestion, unfortunately.

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

...

As far as I can tell they're in the original order. But what do you mean
by "back into their original lines"?

Each line of my data.frame represents a record - except for the first one which 
is the header. Each record has different addresses in the field / column I'm 
analyzing. In fact, the records vary in the number of addresses they feature 
(The first has eight, the second only one, etc.). I don't want a simple list of 
all the country names but a new field in my data.frame which contains for each 
record the country name(s) extracted from the addresses of that very same 
record.
I'd like to measure the number of elements after applying strsplit() to each 
string. I tried:

...
results<- strsplit(results, ";")
numbers<- sapply(results, length)
results<- unlist(results)
...

But this doesn't seem to work, because:

numbers

   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
...

Does anybody know how I would achieve these results instead:

numbers[1]

  [1] 8

numbers[2]

  [1] 1

results[1]

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

results[2]

  [1] "GERMANY"

Thank you very much in advance!

Faithfully yours,

Sabina Arndt

PS: I updated the subject of my message to reflect the progress I've made 
thanks to your replies. I hope this is appropriate and clearer this way.

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.ar...@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


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Re: [R] Relist strings? [Was: How to remove square brackets, etc. from address strings?]

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