[R] rle with data.table - is it possible?
Kate Ignatius
kate.ignatius at gmail.com
Sun Jan 4 04:25:26 CET 2015
Ahh ... you may have missed this:
Larger example below.
So for the below example it will be:
Dad Mum Child Group sumdad summum sumchild childseg
1: AA RR RA A 2 2 0 0
2: AA RR RR A 2 2 1 1
3: AA AA AA B 4 5 5 1
4: AA AA RA B 4 5 5 0
5: RA AA RR B 0 5 5 2
6: RR AA RR B 4 5 5 2
7: AA AA AA B 4 5 5 2
8: AA AA AA C 3 3 0 1
9: AA AA RA C 3 3 0 0
10: AA RR RR C 3 3 0 2
11: AA RR RA C 2 2 0 0
12: AA RR RR C 2 2 1 3
13: AA AA AA C 4 5 5 3
14: AA AA RA C 4 5 5 0
15: RA AA RR C 0 5 5 4
Short explanation: I'm only posting something small here to
make it simple. But I have of course many more Groups but essentially I want to
assign a sequence value to consecutive rows where sumchild is not
equal to 0. As the data frame I'm working with is much larger, this
goes up to 100 maybe even 200 and I have many different groups 20K+.
I would like to do this for every group, not for the whole data frame.
So hence the initial question of asking whether rle and data.table can
be used together.
On Sat, Jan 3, 2015 at 2:45 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:
> Here is what I get when I try to use your algorithm:
>
> myf <- function( s ) {
> seg <- rep( 0, length( s ) )
> rs <- rle( s )
> span <- rs$lengths[ rs$values ]
> seg[ s ] <- rep( seq_along( span ), times = span )
> seg
> }
>
> DT <- data.table( x )
> DT[ , dadseg := myf( Dad %in% c( "AA", "RR" ) ), by=Group ]
> DT[ , mumseg := myf( Mum %in% c( "AA", "RR" ) ), by=Group ]
> DT[ , childseg := myf( Child %in% c( "AA", "RR" ) ), by=Group ]
>>
>> DT
>
> Dad Mum Child Group dadseg mumseg childseg
> 1: AA RR RA A 1 1 0
> 2: AA RR RR A 1 1 1
> 3: AA AA AA B 1 1 1
> 4: AA AA AA B 1 1 1
> 5: RA AA RR B 0 1 1
> 6: RR AA RR B 2 1 1
> 7: AA AA AA B 2 1 1
> 8: AA AA RA C 1 1 0
> 9: AA AA RA C 1 1 0
> 10: AA RR RA C 1 1 0
>
>
>
> On Fri, 2 Jan 2015, Jeff Newmiller wrote:
>
>> The problem is that I cannot see how your use of rle and/or seq_along
>> could possibly lead to the sample result you are giving us. That is why I
>> asked for a new example.
>>
>> ---------------------------------------------------------------------------
>> Jeff Newmiller The ..... ..... Go
>> Live...
>> DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live
>> Go...
>> Live: OO#.. Dead: OO#.. Playing
>> Research Engineer (Solar/Batteries O.O#. #.O#. with
>> /Software/Embedded Controllers) .OO#. .OO#.
>> rocks...1k
>>
>> ---------------------------------------------------------------------------
>> Sent from my phone. Please excuse my brevity.
>>
>> On January 2, 2015 5:11:09 PM PST, Beejai <kate.ignatius at gmail.com> wrote:
>>>
>>> Obviously this is why I need help...
>>>
>>> This is a larger data frame. I'm only posting something small here to
>>> make it simple. There are many Groups which are larger, and I want to
>>> assign a sequence value to consecutive rows where sumchild in not
>>> equal to 0. As the data frame I'm working with is much larger, this
>>> goes up to 100 maybe even 200 and I have many different groups 20K+.
>>> I would like to do this for every group, not for the whole data frame.
>>>
>>> There is no particular science behind this, only data organizing.
>>>
>>> So just say we had data like so:
>>>
>>> Dad Mum Child Group sumdad summum sumchild childseg
>>> 1: AA RR RA A 2 2 0 0
>>> 2: AA RR RR A 2 2 1 1
>>> 3: AA AA AA B 4 5 5 1
>>> 4: AA AA RA B 4 5 5 0
>>> 5: RA AA RR B 0 5 5 2
>>> 6: RR AA RR B 4 5 5 2
>>> 7: AA AA AA B 4 5 5 2
>>> 8: AA AA AA C 3 3 0 1
>>> 9: AA AA RA C 3 3 0 0
>>> 10: AA RR RR C 3 3 0 2
>>> 11: AA RR RA C 2 2 0 0
>>> 12: AA RR RR C 2 2 1 3
>>> 13: AA AA AA C 4 5 5 3
>>> 14: AA AA RA C 4 5 5 0
>>> 15: RA AA RR C 0 5 5 4
>>>
>>> On Fri, Jan 2, 2015 at 12:29 PM, David Winsemius [via R]
>>> <ml-node+s789695n4701316h51 at n4.nabble.com> wrote:
>>>>
>>>>
>>>> On Jan 2, 2015, at 12:07 AM, Kate Ignatius wrote:
>>>>
>>>>> Ah, crap. Yep you're right. This is not going too well. Okay - let
>>>>> me try that again:
>>>>>
>>>>> x$childseg<-0
>>>>> x<-x$sumchild !=0
>>>>
>>>>
>>>> That previous line would appear to overwrite the entire dataframe
>>>
>>> with the
>>>>
>>>> value of one vector
>>>>
>>>>> span<-rle(x)$lengths[rle(x)$values==TRUE]
>>>>> x$childseg[x]<-rep(seq_along(span), times = span)
>>>>>
>>>>> Does this one have any errors?
>>>>
>>>> Even assuming that the code from Jeff Newmiller is creating those
>>>
>>> objects I
>>>>
>>>> get
>>>>
>>>>> x$childseg[x]<-rep(seq_along(span), times = span)
>>>>
>>>> Error in `*tmp*`$childseg : $ operator is invalid for atomic vectors
>>>>
>>>> In the last line you are indexing a vector with a dataframe (or
>>>
>>> perhaps a
>>>>
>>>> data.table).
>>>>
>>>> If we use Newmiller's object and then change some of the instances of
>>>
>>> "x" in
>>>>
>>>> your code to DT we get:
>>>>
>>>>> DT$childseg<-0
>>>>> x<-DT$sumchild !=0 # Try not to overwrite your data-objects
>>>>> span<-rle(x)$lengths[rle(x)$values==TRUE]
>>>>> DT$childseg[x]<-rep(seq_along(span), times = span)
>>>>> DT
>>>>
>>>> Dad Mum Child Group sumdad summum sumchild childseg
>>>> 1: AA RR RA A 2 2 0 0
>>>> 2: AA RR RR A 2 2 1 1
>>>> 3: AA AA AA B 4 5 5 1
>>>> 4: AA AA AA B 4 5 5 1
>>>> 5: RA AA RR B 0 5 5 1
>>>> 6: RR AA RR B 4 5 5 1
>>>> 7: AA AA AA B 4 5 5 1
>>>> 8: AA AA RA C 3 3 0 0
>>>> 9: AA AA RA C 3 3 0 0
>>>> 10: AA RR RA C 3 3 0 0
>>>>
>>>> You persist in posting code where you do not explain what you are
>>>
>>> trying to
>>>>
>>>> do with it. You have already been told that your earlier efforts
>>>
>>> using `rle`
>>>>
>>>> did not make any sense. Post a complete example and then explain what
>>>
>>> you
>>>>
>>>> desire as an object. It's often helpful to provide a scientific
>>>
>>> background
>>>>
>>>> for what the data represents.
>>>>
>>>> --
>>>> David.
>>>>
>>>>>
>>>>>
>>>>> On Fri, Jan 2, 2015 at 2:32 AM, David Winsemius <[hidden email]>
>>>
>>> wrote:
>>>>>>
>>>>>>
>>>>>>> On Jan 1, 2015, at 5:07 PM, Kate Ignatius <[hidden email]> wrote:
>>>>>>>
>>>>>>> Apologies - mix up of syntax all over the place, a habit of mine.
>>>
>>> The
>>>>>>>
>>>>>>> last line was in there because of code beforehand so it really
>>>
>>> doesn't
>>>>>>>
>>>>>>> need to be there. Here is the proper code I hope:
>>>>>>>
>>>>>>> childseg<-0
>>>>>>> x<-sumchild ==0
>>>>>>> span<-rle(x)$lengths[rle(x)$values==TRUE]
>>>>>>> childseg[x]<-rep(seq_along(span), times = span)
>>>>>>>
>>>>>>
>>>>>> This remains not reproducible. We have no idea what sumchild might
>>>
>>> be and
>>>>>>
>>>>>> the code throws an error. My guess is that you are trying to get a
>>>
>>> result
>>>>>>
>>>>>> such as would be delivered by:
>>>>>>
>>>>>> childseg <- sumchild[ sumchild != 0 ]
>>>>>>
>>>>>> ?
>>>>>> David.
>>>>>>
>>>>>>>
>>>>>>> On Thu, Jan 1, 2015 at 12:13 PM, Jeff Newmiller
>>>>>>> <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Thank you for attempting to encode what you want using R syntax,
>>>
>>> but
>>>>>>>>
>>>>>>>> you are not really succeeding yet (too many errors). Perhaps
>>>
>>> another hand
>>>>>>>>
>>>>>>>> generated result would help? A new input data frame might or
>>>
>>> might not be
>>>>>>>>
>>>>>>>> needed to illustrate desired results.
>>>>>>>>
>>>>>>>> Your second and third lines are syntactically incorrect, and I
>>>
>>> don't
>>>>>>>>
>>>>>>>> understand what you hope to accomplish by assigning an empty
>>>
>>> string to a
>>>>>>>>
>>>>>>>> numeric in your last line.
>>>>>>>>
>>>>>>>>
>>>
>>> ---------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> Jeff Newmiller The ..... .....
>>>
>>> Go
>>>>>>>>
>>>>>>>> Live...
>>>>>>>> DCN:<[hidden email]> Basics: ##.#. ##.#. Live Go...
>>>>>>>> Live: OO#.. Dead: OO#..
>>>
>>> Playing
>>>>>>>>
>>>>>>>> Research Engineer (Solar/Batteries O.O#. #.O#.
>>>
>>> with
>>>>>>>>
>>>>>>>> /Software/Embedded Controllers) .OO#. .OO#.
>>>>>>>> rocks...1k
>>>>>>>>
>>>>>>>>
>>>
>>> ---------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> Sent from my phone. Please excuse my brevity.
>>>>>>>>
>>>>>>>> On January 1, 2015 4:16:52 AM PST, Kate Ignatius <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Is it possible to add the following code or similar in
>>>
>>> data.table:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> childseg<-0
>>>>>>>>> x:=sumchild <-0
>>>>>>>>> span<-rle(x)$lengths[rle(x)$values==TRUE
>>>>>>>>> childseg[x]<-rep(seq_along(span), times = span)
>>>>>>>>> childseg[childseg == 0]<-''
>>>>>>>>>
>>>>>>>>> I was hoping to do this code by Group for mum, dad and
>>>>>>>>> child. The problem I'm having is with the
>>>>>>>>> span<-rle(x)$lengths[rle(x)$values==TRUE line which I'm not sure
>>>
>>> can
>>>>>>>>>
>>>>>>>>> be added to data.table.
>>>>>>>>>
>>>>>>>>> [Previous email had incorrect code]
>>>>>>>>>
>>>>>>>>> On Wed, Dec 31, 2014 at 3:45 AM, Jeff Newmiller
>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>
>>>>>>>>>> I do not understand the value of using the rle function in your
>>>>>>>>>
>>>>>>>>> description,
>>>>>>>>>>
>>>>>>>>>> but the code below appears to produce the table you want.
>>>>>>>>>>
>>>>>>>>>> Note that better support for the data.table package might be
>>>
>>> found at
>>>>>>>>>>
>>>>>>>>>> stackexchange as the documentation specifies.
>>>>>>>>>>
>>>>>>>>>> x <- read.table( text=
>>>>>>>>>> "Dad Mum Child Group
>>>>>>>>>> AA RR RA A
>>>>>>>>>> AA RR RR A
>>>>>>>>>> AA AA AA B
>>>>>>>>>> AA AA AA B
>>>>>>>>>> RA AA RR B
>>>>>>>>>> RR AA RR B
>>>>>>>>>> AA AA AA B
>>>>>>>>>> AA AA RA C
>>>>>>>>>> AA AA RA C
>>>>>>>>>> AA RR RA C
>>>>>>>>>> ", header=TRUE, stringsAsFactors=FALSE )
>>>>>>>>>>
>>>>>>>>>> library(data.table)
>>>>>>>>>> DT <- data.table( x )
>>>>>>>>>> DT[ , cdad := as.integer( Dad %in% c( "AA", "RR" ) ) ]
>>>>>>>>>> DT[ , sumdad := 0L ]
>>>>>>>>>> DT[ 1==DT$cdad, sumdad := sum( cdad ), by=Group ]
>>>>>>>>>> DT[ , cdad := NULL ]
>>>>>>>>>> DT[ , cmum := as.integer( Mum %in% c( "AA", "RR" ) ) ]
>>>>>>>>>> DT[ , summum := 0L ]
>>>>>>>>>> DT[ 1==DT$cmum, summum := sum( cmum ), by=Group ]
>>>>>>>>>> DT[ , cmum := NULL ]
>>>>>>>>>> DT[ , cchild := as.integer( Child %in% c( "AA", "RR" ) ) ]
>>>>>>>>>> DT[ , sumchild := 0L ]
>>>>>>>>>> DT[ 1==DT$cchild, sumchild := sum( cchild ), by=Group ]
>>>>>>>>>> DT[ , cchild := NULL ]
>>>>>>>>>>
>>>>>>>>>>> DT
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Dad Mum Child Group sumdad summum sumchild
>>>>>>>>>> 1: AA RR RA A 2 2 0
>>>>>>>>>> 2: AA RR RR A 2 2 1
>>>>>>>>>> 3: AA AA AA B 4 5 5
>>>>>>>>>> 4: AA AA AA B 4 5 5
>>>>>>>>>> 5: RA AA RR B 0 5 5
>>>>>>>>>> 6: RR AA RR B 4 5 5
>>>>>>>>>> 7: AA AA AA B 4 5 5
>>>>>>>>>> 8: AA AA RA C 3 3 0
>>>>>>>>>> 9: AA AA RA C 3 3 0
>>>>>>>>>> 10: AA RR RA C 3 3 0
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Tue, 30 Dec 2014, Kate Ignatius wrote:
>>>>>>>>>>
>>>>>>>>>>> I'm trying to use both these packages and wondering whether
>>>
>>> they are
>>>>>>>>>>>
>>>>>>>>>>> possible...
>>>>>>>>>>>
>>>>>>>>>>> To make this simple, my ultimate goal is determine long
>>>
>>> stretches of
>>>>>>>>>>>
>>>>>>>>>>> 1s, but I want to do this within groups (hence using the
>>>
>>> data.table
>>>>>>>>>
>>>>>>>>> as
>>>>>>>>>>>
>>>>>>>>>>> I use the "set key" option. However, I'm I'm not having much
>>>
>>> luck
>>>>>>>>>>>
>>>>>>>>>>> making this possible.
>>>>>>>>>>>
>>>>>>>>>>> For example, for simplistic sake, I have the following data:
>>>>>>>>>>>
>>>>>>>>>>> Dad Mum Child Group
>>>>>>>>>>> AA RR RA A
>>>>>>>>>>> AA RR RR A
>>>>>>>>>>> AA AA AA B
>>>>>>>>>>> AA AA AA B
>>>>>>>>>>> RA AA RR B
>>>>>>>>>>> RR AA RR B
>>>>>>>>>>> AA AA AA B
>>>>>>>>>>> AA AA RA C
>>>>>>>>>>> AA AA RA C
>>>>>>>>>>> AA RR RA C
>>>>>>>>>>>
>>>>>>>>>>> And the following code which I know works
>>>>>>>>>>>
>>>>>>>>>>> hetdad <- as.numeric(x[c(1)]=="AA" | x[c(1)]=="RR")
>>>>>>>>>>> sumdad <- rle(hetdad)$lengths[rle(hetdad)$values==1]
>>>>>>>>>>>
>>>>>>>>>>> hetmum <- as.numeric(x[c(2)]=="AA" | x[c(2)]=="RR")
>>>>>>>>>>> summum <- rle(hetmum)$lengths[rle(hetmum)$values==1]
>>>>>>>>>>>
>>>>>>>>>>> hetchild <- as.numeric(x[c(3)]=="AA" | x[c(3)]=="RR")
>>>>>>>>>>> sumchild <- rle(hetchild)$lengths[rle(hetchild)$values==1]
>>>>>>>>>>>
>>>>>>>>>>> However, I wish to do the above code by Group (though this
>>>
>>> file is
>>>>>>>>>>>
>>>>>>>>>>> millions of rows long and groups will be larger but just
>>>
>>> wanted to
>>>>>>>>>>>
>>>>>>>>>>> simply the example).
>>>>>>>>>>>
>>>>>>>>>>> I did something like this but of course I got an error:
>>>>>>>>>>>
>>>>>>>>>>> LOH[,hetdad:=as.numeric(x[c(1)]=="AA" | x[c(1)]=="RR")]
>>>>>>>>>>>
>>> LOH[,sumdad:=rle(hetdad)$lengths[rle(hetdad)$values==1],by=Group]
>>>>>>>>>>>
>>>>>>>>>>> LOH[,hetmum:=as.numeric(x[c(2)]=="AA" | x[c(2)]=="RR")]
>>>>>>>>>>>
>>> LOH[,summum:=rle(hetmum)$lengths[rle(hetmum)$values==1],by=Group]
>>>>>>>>>>>
>>>>>>>>>>> LOH[,hetchild:=as.numeric(x[c(3)]=="AA" | x[c(3)]=="RR")]
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>> LOH[,sumchild:=rle(hetchild)$lengths[rle(hetchild)$values==1],by=Group]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The reason being as I want to eventually have something like
>>>
>>> this:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Dad Mum Child Group sumdad summum sumchild
>>>>>>>>>>> AA RR RA A 2 2 0
>>>>>>>>>>> AA RR RR A 2 2 1
>>>>>>>>>>> AA AA AA B 4 5 5
>>>>>>>>>>> AA AA AA B 4 5 5
>>>>>>>>>>> RA AA RR B 0 5 5
>>>>>>>>>>> RR AA RR B 4 5 5
>>>>>>>>>>> AA AA AA B 4 5 5
>>>>>>>>>>> AA AA RA C 3 3 0
>>>>>>>>>>> AA AA RA C 3 3 0
>>>>>>>>>>> AA RR RA C 3 3 0
>>>>>>>>>>>
>>>>>>>>>>> That is, I would like to have the specific counts next to what
>>>
>>> I'm
>>>>>>>>>>>
>>>>>>>>>>> consecutively counting per group. So for Group A for dad
>>>
>>> there are
>>>>>>>>>
>>>>>>>>> 2
>>>>>>>>>>>
>>>>>>>>>>> AAs, there are two RRs for mum but only 1 AA or RR for the
>>>
>>> child
>>>>>>>>>
>>>>>>>>> and
>>>>>>>>>>>
>>>>>>>>>>> that is RR (so the 1 is next to the RR and not the RA).
>>>>>>>>>>>
>>>>>>>>>>> Can this be done?
>>>>>>>>>>>
>>>>>>>>>>> K.
>>>>>>>>>>>
>>>>>>>>>>> ______________________________________________
>>>>>>>>>>> [hidden email] 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.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>
>>> ---------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>> Jeff Newmiller The ..... .....
>>>
>>> Go
>>>>>>>>>
>>>>>>>>> Live...
>>>>>>>>>>
>>>>>>>>>> DCN:<[hidden email]> Basics: ##.#. ##.#. Live
>>>>>>>>>
>>>>>>>>> Go...
>>>>>>>>>>
>>>>>>>>>> Live: OO#.. Dead: OO#..
>>>>>>>>>
>>>>>>>>> Playing
>>>>>>>>>>
>>>>>>>>>> Research Engineer (Solar/Batteries O.O#. #.O#.
>>>
>>> with
>>>>>>>>>>
>>>>>>>>>> /Software/Embedded Controllers) .OO#. .OO#.
>>>>>>>>>
>>>>>>>>> rocks...1k
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>
>>> ---------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> [hidden email] 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.
>>>>>>
>>>>>>
>>>>
>>>> David Winsemius
>>>> Alameda, CA, USA
>>>>
>>>> ______________________________________________
>>>> [hidden email] 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.
>>>>
>>>>
>>>> ________________________________
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>>>>
>>>> NAML
>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>>
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>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>>> PLEASE do read the posting guide
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>>
>>
>> ______________________________________________
>> 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.
>
>
> ---------------------------------------------------------------------------
> Jeff Newmiller The ..... ..... Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
> Live: OO#.. Dead: OO#.. Playing
> Research Engineer (Solar/Batteries O.O#. #.O#. with
> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
> ---------------------------------------------------------------------------
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