[R] rle with data.table - is it possible?
Jeff Newmiller
jdnewmil at dcn.davis.CA.us
Thu Jan 1 18:13:31 CET 2015
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.
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Sent from my phone. Please excuse my brevity.
On January 1, 2015 4:16:52 AM PST, Kate Ignatius <kate.ignatius at gmail.com> 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
><jdnewmil at dcn.davis.ca.us> 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.
>>>
>>> ______________________________________________
>>> 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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