R help - Sep 2016 - element wise pattern recognition and string substitution

Jun:

You need to provide a clear specification via regular expressions of
the patterns you wish to match -- at least for me to decipher it.
Others may be smarter than I, though...

Jeff: Thanks. I have now convinced myself that it can be done (a
"proof" of sorts): If pat1, pat2,..., patn are m different patterns
(in a vector of patterns)  to be matched in a vector of n strings,
where only one of the patterns will match in any string,  then use
paste() (probably via do.call()) or otherwise to paste them together
separated by "|" to form the concatenated pattern, pat. Then

sub(paste0("^.*(",pat, ").*$"),"\\1",thevector)

should extract the matching pattern in each (perhaps with a little
fiddling due to precedence rules); e.g.
> z <-c(".fg.h.g.a.a", "bb..dd.ef.tgf.",
"foo...b.bbb.tgy")
> pat1 <- "a+\\.*a+"
> pat2 <-"b+\\.*b+"
> pat <- c(pat1,pat2)
> pat <- do.call(paste,c(as.list(pat), sep="|"))
> pat
[1] "a+\\.*a+|b+\\.*b+"
> sub(paste0("^[^b]*(",pat,").*$"), "\\1", z)
[1] "a.a"   "bb"    "b.bbb"

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Sep 5, 2016 at 9:56 AM, Jun Shen <jun.shen.ut at gmail.com>
wrote:
> Thanks for the reply, Bert.
>
> Your solution solves the example. I actually have a more general situation
> where I have this dot concatenated string from multiple variables. The
> problem is those variables may have values with dots in there. The number
of
> dots are not consistent for all values of a variable. So I am thinking to
> define a vector of patterns for the vector of the string and hopefully to
> find a way to use a pattern from the pattern vector for each value of the
> string vector. The only way I can think of is "for" loop, which
can be slow.
> Also these are happening in a function I am writing. Just wonder if there
is
> another more efficient way. Thanks a lot.
>
> Jun
>
> On Mon, Sep 5, 2016 at 1:41 AM, Bert Gunter <bgunter.4567 at
gmail.com> wrote:
>>
>> Well, he did provide an example, and...
>>
>>
>> > z <- c('TX.WT.CUT.mean','mg.tx.cv')
>>
>> > sub("^.+?\\.(.+)\\.[^.]+$","\\1",z)
>> [1] "WT.CUT" "tx"
>>
>>
>> ## seems to do what was requested.
>>
>> Jeff would have to amplify on his initial statement however: do you
>> mean that separate patterns can always be combined via "|" ? 
Or
>> something deeper?
>>
>> Cheers,
>> Bert
>> Bert Gunter
>>
>> "The trouble with having an open mind is that people keep coming
along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic
strip )
>>
>>
>> On Sun, Sep 4, 2016 at 9:30 PM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us>
>> wrote:
>> > Your opening assertion is false.
>> >
>> > Provide a reproducible example and someone will demonstrate.
>> > --
>> > Sent from my phone. Please excuse my brevity.
>> >
>> > On September 4, 2016 9:06:59 PM PDT, Jun Shen <jun.shen.ut at
gmail.com>
>> > wrote:
>> >>Dear list,
>> >>
>> >>I have a vector of strings that cannot be described by one
pattern. So
>> >>let's say I construct a vector of patterns in the same
length as the
>> >>vector
>> >>of strings, can I do the element wise pattern recognition and
string
>> >>substitution.
>> >>
>> >>For example,
>> >>
>> >>pattern1 <- "([^.]*)\\.([^.]*\\.[^.]*)\\.(.*)"
>> >>pattern2 <- "([^.]*)\\.([^.]*)\\.(.*)"
>> >>
>> >>patterns <- c(pattern1,pattern2)
>> >>strings <- c('TX.WT.CUT.mean','mg.tx.cv')
>> >>
>> >>Say I want to extract "WT.CUT" from the first string
and "tx" from the
>> >>second string. If I do
>> >>
>> >>sub(patterns, '\\2', strings), only the first pattern
will be used.
>> >>
>> >>looping the patterns doesn't work the way I want.
Appreciate any
>> >>comments.
>> >>Thanks.
>> >>
>> >>Jun
>> >>
>> >>       [[alternative HTML version deleted]]
>> >>
>> >>______________________________________________
>> >>R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>> >>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.
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>> > 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.
>
>

Just noticed: My clumsy do.call() line in my previously posted code
below should be replaced with:
pat <- paste(pat,collapse = "|")

> pat <- c(pat1,pat2)
> paste(pat,collapse="|")
[1] "a+\\.*a+|b+\\.*b+"

************ replace this **************************
> pat <- do.call(paste,c(as.list(pat), sep="|"))
********************************************
> sub(paste0("^[^b]*(",pat,").*$"),"\\1",z)
[1] "a.a"   "bb"    "b.bbb"


-- Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Sep 5, 2016 at 12:11 PM, Bert Gunter <bgunter.4567 at gmail.com>
wrote:
> Jun:
>
> You need to provide a clear specification via regular expressions of
> the patterns you wish to match -- at least for me to decipher it.
> Others may be smarter than I, though...
>
> Jeff: Thanks. I have now convinced myself that it can be done (a
> "proof" of sorts): If pat1, pat2,..., patn are m different
patterns
> (in a vector of patterns)  to be matched in a vector of n strings,
> where only one of the patterns will match in any string,  then use
> paste() (probably via do.call()) or otherwise to paste them together
> separated by "|" to form the concatenated pattern, pat. Then
>
> sub(paste0("^.*(",pat,
").*$"),"\\1",thevector)
>
> should extract the matching pattern in each (perhaps with a little
> fiddling due to precedence rules); e.g.
>
>> z <-c(".fg.h.g.a.a", "bb..dd.ef.tgf.",
"foo...b.bbb.tgy")
>
>> pat1 <- "a+\\.*a+"
>> pat2 <-"b+\\.*b+"
>> pat <- c(pat1,pat2)
>
>> pat <- do.call(paste,c(as.list(pat), sep="|"))
>> pat
> [1] "a+\\.*a+|b+\\.*b+"
>
>> sub(paste0("^[^b]*(",pat,").*$"), "\\1",
z)
> [1] "a.a"   "bb"    "b.bbb"
>
> Cheers,
> Bert
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip
)
>
>
> On Mon, Sep 5, 2016 at 9:56 AM, Jun Shen <jun.shen.ut at gmail.com>
wrote:
>> Thanks for the reply, Bert.
>>
>> Your solution solves the example. I actually have a more general
situation
>> where I have this dot concatenated string from multiple variables. The
>> problem is those variables may have values with dots in there. The
number of
>> dots are not consistent for all values of a variable. So I am thinking
to
>> define a vector of patterns for the vector of the string and hopefully
to
>> find a way to use a pattern from the pattern vector for each value of
the
>> string vector. The only way I can think of is "for" loop,
which can be slow.
>> Also these are happening in a function I am writing. Just wonder if
there is
>> another more efficient way. Thanks a lot.
>>
>> Jun
>>
>> On Mon, Sep 5, 2016 at 1:41 AM, Bert Gunter <bgunter.4567 at
gmail.com> wrote:
>>>
>>> Well, he did provide an example, and...
>>>
>>>
>>> > z <- c('TX.WT.CUT.mean','mg.tx.cv')
>>>
>>> > sub("^.+?\\.(.+)\\.[^.]+$","\\1",z)
>>> [1] "WT.CUT" "tx"
>>>
>>>
>>> ## seems to do what was requested.
>>>
>>> Jeff would have to amplify on his initial statement however: do you
>>> mean that separate patterns can always be combined via
"|" ?  Or
>>> something deeper?
>>>
>>> Cheers,
>>> Bert
>>> Bert Gunter
>>>
>>> "The trouble with having an open mind is that people keep
coming along
>>> and sticking things into it."
>>> -- Opus (aka Berkeley Breathed in his "Bloom County"
comic strip )
>>>
>>>
>>> On Sun, Sep 4, 2016 at 9:30 PM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us>
>>> wrote:
>>> > Your opening assertion is false.
>>> >
>>> > Provide a reproducible example and someone will demonstrate.
>>> > --
>>> > Sent from my phone. Please excuse my brevity.
>>> >
>>> > On September 4, 2016 9:06:59 PM PDT, Jun Shen <jun.shen.ut
at gmail.com>
>>> > wrote:
>>> >>Dear list,
>>> >>
>>> >>I have a vector of strings that cannot be described by one
pattern. So
>>> >>let's say I construct a vector of patterns in the same
length as the
>>> >>vector
>>> >>of strings, can I do the element wise pattern recognition
and string
>>> >>substitution.
>>> >>
>>> >>For example,
>>> >>
>>> >>pattern1 <- "([^.]*)\\.([^.]*\\.[^.]*)\\.(.*)"
>>> >>pattern2 <- "([^.]*)\\.([^.]*)\\.(.*)"
>>> >>
>>> >>patterns <- c(pattern1,pattern2)
>>> >>strings <-
c('TX.WT.CUT.mean','mg.tx.cv')
>>> >>
>>> >>Say I want to extract "WT.CUT" from the first
string and "tx" from the
>>> >>second string. If I do
>>> >>
>>> >>sub(patterns, '\\2', strings), only the first
pattern will be used.
>>> >>
>>> >>looping the patterns doesn't work the way I want.
Appreciate any
>>> >>comments.
>>> >>Thanks.
>>> >>
>>> >>Jun
>>> >>
>>> >>       [[alternative HTML version deleted]]
>>> >>
>>> >>______________________________________________
>>> >>R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>> >>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.
>>> >
>>> > ______________________________________________
>>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>> > 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.
>>
>>

Hi Bert,

I still couldn't make the multiple patterns to work. Here is an example. I
make the pattern as follows

final.pattern <-
"(240\\.m\\.g)\\.(>50-70\\.kg)\\.(.*)|(3\\.mg\\.kg)\\.(>50-70\\.kg)\\.(.*)|(240\\.m\\.g)\\.(>70-90\\.kg)\\.(.*)|(3\\.mg\\.kg)\\.(>70-90\\.kg)\\.(.*)|(240\\.m\\.g)\\.(>90-110\\.kg)\\.(.*)|(3\\.mg\\.kg)\\.(>90-110\\.kg)\\.(.*)|(240\\.m\\.g)\\.(50\\.kg\\.or\\.less)\\.(.*)|(3\\.mg\\.kg)\\.(50\\.kg\\.or\\.less)\\.(.*)|(240\\.m\\.g)\\.(>110\\.kg)\\.(.*)|(3\\.mg\\.kg)\\.(>110\\.kg)\\.(.*)"

test.string <- c('240.m.g.>110.kg.geo.mean',
'3.mg.kg.>110.kg.P05',
'240.m.g.>50-70.kg.geo.mean')

sub(final.pattern, '\\1', test.string)
sub(final.pattern, '\\2', test.string)
sub(final.pattern, '\\3', test.string)

Only the third string has been correctly parsed, which matches the
first pattern. It seems the rest of the patterns are not called.

Jun


On Mon, Sep 5, 2016 at 10:21 PM, Bert Gunter <bgunter.4567 at gmail.com>
wrote:
> Just noticed: My clumsy do.call() line in my previously posted code
> below should be replaced with:
> pat <- paste(pat,collapse = "|")
>
>
> > pat <- c(pat1,pat2)
> > paste(pat,collapse="|")
> [1] "a+\\.*a+|b+\\.*b+"
>
> ************ replace this **************************
> > pat <- do.call(paste,c(as.list(pat), sep="|"))
> ********************************************
> >
sub(paste0("^[^b]*(",pat,").*$"),"\\1",z)
> [1] "a.a"   "bb"    "b.bbb"
>
>
> -- Bert
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip
)
>
>
> On Mon, Sep 5, 2016 at 12:11 PM, Bert Gunter <bgunter.4567 at
gmail.com>
> wrote:
> > Jun:
> >
> > You need to provide a clear specification via regular expressions of
> > the patterns you wish to match -- at least for me to decipher it.
> > Others may be smarter than I, though...
> >
> > Jeff: Thanks. I have now convinced myself that it can be done (a
> > "proof" of sorts): If pat1, pat2,..., patn are m different
patterns
> > (in a vector of patterns)  to be matched in a vector of n strings,
> > where only one of the patterns will match in any string,  then use
> > paste() (probably via do.call()) or otherwise to paste them together
> > separated by "|" to form the concatenated pattern, pat. Then
> >
> > sub(paste0("^.*(",pat,
").*$"),"\\1",thevector)
> >
> > should extract the matching pattern in each (perhaps with a little
> > fiddling due to precedence rules); e.g.
> >
> >> z <-c(".fg.h.g.a.a", "bb..dd.ef.tgf.",
"foo...b.bbb.tgy")
> >
> >> pat1 <- "a+\\.*a+"
> >> pat2 <-"b+\\.*b+"
> >> pat <- c(pat1,pat2)
> >
> >> pat <- do.call(paste,c(as.list(pat), sep="|"))
> >> pat
> > [1] "a+\\.*a+|b+\\.*b+"
> >
> >> sub(paste0("^[^b]*(",pat,").*$"),
"\\1", z)
> > [1] "a.a"   "bb"    "b.bbb"
> >
> > Cheers,
> > Bert
> >
> >
> > Bert Gunter
> >
> > "The trouble with having an open mind is that people keep coming
along
> > and sticking things into it."
> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic
strip )
> >
> >
> > On Mon, Sep 5, 2016 at 9:56 AM, Jun Shen <jun.shen.ut at
gmail.com> wrote:
> >> Thanks for the reply, Bert.
> >>
> >> Your solution solves the example. I actually have a more general
> situation
> >> where I have this dot concatenated string from multiple variables.
The
> >> problem is those variables may have values with dots in there. The
> number of
> >> dots are not consistent for all values of a variable. So I am
thinking
> to
> >> define a vector of patterns for the vector of the string and
hopefully
> to
> >> find a way to use a pattern from the pattern vector for each value
of
> the
> >> string vector. The only way I can think of is "for"
loop, which can be
> slow.
> >> Also these are happening in a function I am writing. Just wonder
if
> there is
> >> another more efficient way. Thanks a lot.
> >>
> >> Jun
> >>
> >> On Mon, Sep 5, 2016 at 1:41 AM, Bert Gunter <bgunter.4567 at
gmail.com>
> wrote:
> >>>
> >>> Well, he did provide an example, and...
> >>>
> >>>
> >>> > z <- c('TX.WT.CUT.mean','mg.tx.cv')
> >>>
> >>> > sub("^.+?\\.(.+)\\.[^.]+$","\\1",z)
> >>> [1] "WT.CUT" "tx"
> >>>
> >>>
> >>> ## seems to do what was requested.
> >>>
> >>> Jeff would have to amplify on his initial statement however:
do you
> >>> mean that separate patterns can always be combined via
"|" ?  Or
> >>> something deeper?
> >>>
> >>> Cheers,
> >>> Bert
> >>> Bert Gunter
> >>>
> >>> "The trouble with having an open mind is that people keep
coming along
> >>> and sticking things into it."
> >>> -- Opus (aka Berkeley Breathed in his "Bloom County"
comic strip )
> >>>
> >>>
> >>> On Sun, Sep 4, 2016 at 9:30 PM, Jeff Newmiller <
> jdnewmil at dcn.davis.ca.us>
> >>> wrote:
> >>> > Your opening assertion is false.
> >>> >
> >>> > Provide a reproducible example and someone will
demonstrate.
> >>> > --
> >>> > Sent from my phone. Please excuse my brevity.
> >>> >
> >>> > On September 4, 2016 9:06:59 PM PDT, Jun Shen
<jun.shen.ut at gmail.com
> >
> >>> > wrote:
> >>> >>Dear list,
> >>> >>
> >>> >>I have a vector of strings that cannot be described by
one pattern.
> So
> >>> >>let's say I construct a vector of patterns in the
same length as the
> >>> >>vector
> >>> >>of strings, can I do the element wise pattern
recognition and string
> >>> >>substitution.
> >>> >>
> >>> >>For example,
> >>> >>
> >>> >>pattern1 <-
"([^.]*)\\.([^.]*\\.[^.]*)\\.(.*)"
> >>> >>pattern2 <- "([^.]*)\\.([^.]*)\\.(.*)"
> >>> >>
> >>> >>patterns <- c(pattern1,pattern2)
> >>> >>strings <-
c('TX.WT.CUT.mean','mg.tx.cv')
> >>> >>
> >>> >>Say I want to extract "WT.CUT" from the
first string and "tx" from
> the
> >>> >>second string. If I do
> >>> >>
> >>> >>sub(patterns, '\\2', strings), only the first
pattern will be used.
> >>> >>
> >>> >>looping the patterns doesn't work the way I want.
Appreciate any
> >>> >>comments.
> >>> >>Thanks.
> >>> >>
> >>> >>Jun
> >>> >>
> >>> >>       [[alternative HTML version deleted]]
> >>> >>
> >>> >>______________________________________________
> >>> >>R-help at r-project.org mailing list -- To UNSUBSCRIBE
and more, see
> >>> >>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.
> >>> >
> >>> > ______________________________________________
> >>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE
and more, see
> >>> > 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.
> >>
> >>
>
	[[alternative HTML version deleted]]