[R] Selecting First Incidence from Longitudinal Data
arun
smartpink111 at yahoo.com
Sun Feb 24 06:45:39 CET 2013
Hi,
I am not sure why you are getting different results. I couldn't reproduce your problem.
dat1<- read.table(text="
ID COMPL SEX HEREDITY
1 0 1 2
1 0 1 2
1 3 1 2
2 0 0 1
2 1 0 1
2 2 0 1
2 2 0 1
3 0 0 1
3 0 0 1
3 0 0 1
3 0 0 1
3 2 0 1
4 0 1 2
4 0 1 2
",sep="",header=TRUE)
do.call(rbind,lapply(split(dat1,dat1$ID),function(x) if(any(x$COMPL!=0)) head(x[x$COMPL!=0,],1) else head(x,1)))
# ID COMPL SEX HEREDITY
#1 1 3 1 2
#2 2 1 0 1
#3 3 2 0 1
#4 4 0 1 2
You could also try:
dat1[with(dat1,ave(COMPL,ID,FUN=function(x) if(any(x!=0)) cumsum(x>0) else seq_along(x)))==1,] #modification of David's code
# ID COMPL SEX HEREDITY
#3 1 3 1 2
#5 2 1 0 1
#12 3 2 0 1
#13 4 0 1 2
A.K.
________________________________
From: Tasnuva Tabassum <t.tasnuva at gmail.com>
To: arun <smartpink111 at yahoo.com>
Sent: Sunday, February 24, 2013 12:08 AM
Subject: Re: [R] Selecting First Incidence from Longitudinal Data
sorry, I tried this. But it gave me answer:
# ID COMPL SEX HEREDITY
#1 1 0 1 2
#4 2 0 0 1
#8 3 0 0 1
#13 4 0 1 2
On Sat, Feb 23, 2013 at 8:44 PM, arun <smartpink111 at yahoo.com> wrote:
Hi,
>Try this:
>#dat1
> do.call(rbind,lapply(split(dat1,dat1$ID),function(x) if(any(x$COMPL!=0)) head(x[x$COMPL!=0,],1) else head(x,1)))
>
># ID COMPL SEX HEREDITY
>
>#1 1 3 1 2
>#2 2 1 0 1
>#3 3 2 0 1
>#4 4 0 1 2
>A.K.
>
>
>
>
>
>
>________________________________
>From: Tasnuva Tabassum <t.tasnuva at gmail.com>
>To: Xiaogang Su <xiaogangsu at gmail.com>
>Cc: arun <smartpink111 at yahoo.com>; R help <r-help at r-project.org>; Rui Barradas <ruipbarradas at sapo.pt>
>Sent: Saturday, February 23, 2013 11:23 PM
>
>Subject: Re: [R] Selecting First Incidence from Longitudinal Data
>
>
>Hi
>Thank you very much, but I forgot to tell that I also want to include the patients for which no complication occurred. That is, for my data I want to include patient no. 4, for which the COMPL value will be 0.
>
>In that case, what R function should I write?
>
>
>
>
>On Sat, Feb 23, 2013 at 12:23 PM, Xiaogang Su <xiaogangsu at gmail.com> wrote:
>
>My bad. I didn't try it out with the real data. Here you go. HTH, X
>>
>>
>>dat <- read.table(text="
>>ID COMPL SEX HEREDITY
>>1 0 1 2
>>1 0 1 2
>>1 3 1 2
>>2 0 0 1
>>2 1 0 1
>>2 2 0 1
>>2 2 0 1
>>3 0 0 1
>>3 0 0 1
>>3 0 0 1
>>3 0 0 1
>>3 2 0 1
>>4 0 1 2
>>4 0 1 2
>>", header = TRUE)
>>
>>
>>dat0 <- dat[dat$COMPL!=0, ]
>>dat0$sequence <- as.vector(unlist(lapply(aggregate(dat0$ID, by=list(dat0$ID),FUN=length)$x, FUN=function(x){seq(1, x)})))
>>dat0 <- dat0[dat0$sequence==1, ]
>>dat0
>>
>>
>>
>>
>>On Sat, Feb 23, 2013 at 2:09 PM, arun <smartpink111 at yahoo.com> wrote:
>>
>>HI,
>>>Tried your approach:
>>>
>>>
>>> dat1$sequence <- as.vector(unlist(lapply( aggregate(dat1$ID, by=list(dat1$ID),FUN=length)$x, FUN=function(x){seq(1, x)})))
>>> dat0 <- dat1[dat1$sequence==1 & dat1$COMPL!= 0, ] #your second solution
>>> dat0
>>>#[1] ID COMPL SEX HEREDITY sequence
>>>#<0 rows> (or 0-length row.names)
>>>
>>>
>>>dat1[dat1$sequence==1,] #here the OP wanted first incidence where COMPL!=0
>>># ID COMPL SEX HEREDITY sequence
>>>#1 1 0 1 2 1
>>>#4 2 0 0 1 1
>>>#8 3 0 0 1 1
>>>#13 4 0 1 2 1
>>>A.K.
>>>
>>>
>>>
>>>
>>>----- Original Message -----
>>>From: Xiaogang Su <xiaogangsu at gmail.com>
>>>To: Rui Barradas <ruipbarradas at sapo.pt>
>>>Cc: r-help at r-project.org
>>>Sent: Saturday, February 23, 2013 2:15 PM
>>>Subject: Re: [R] Selecting First Incidence from Longitudinal Data
>>>
>>>Try this:
>>>dat$sequence <- as.vector(unlist(lapply( aggregate(dat$ID, by=list(x),
>>>FUN=length)$x, FUN=function(x){seq(1, x))))
>>>dat0 <- dat[dat$sequence==1, ]
>>>
>>>HTH, X
>>>
>>>
>>>On Sat, Feb 23, 2013 at 1:07 PM, Rui Barradas <ruipbarradas at sapo.pt> wrote:
>>>
>>>> Hello,
>>>>
>>>> You can use ?aggregate and ?head to do what you want. Try the following.
>>>>
>>>>
>>>>
>>>> dat <- read.table(text="
>>>>
>>>> ID COMPL SEX HEREDITY
>>>> 1 0 1 2
>>>> 1 0 1 2
>>>> 1 3 1 2
>>>> 2 0 0 1
>>>> 2 1 0 1
>>>> 2 2 0 1
>>>> 2 2 0 1
>>>> 3 0 0 1
>>>> 3 0 0 1
>>>> 3 0 0 1
>>>> 3 0 0 1
>>>> 3 2 0 1
>>>> 4 0 1 2
>>>> 4 0 1 2
>>>> ", header = TRUE)
>>>>
>>>> aggregate(. ~ ID, data = subset(dat, COMPL != 0), head, 1)
>>>>
>>>>
>>>> Hope this helps,
>>>>
>>>> Rui Barradas
>>>>
>>>> Em 23-02-2013 14:28, Tasnuva Tabassum escreveu:
>>>>
>>>> I have a longitudinal competing risk data of the form:
>>>>>
>>>>> ID COMPL SEX HEREDITY
>>>>> 1 0 1 2
>>>>> 1 0 1 2
>>>>> 1 3 1 2
>>>>> 2 0 0 1
>>>>> 2 1 0 1
>>>>> 2 2 0 1
>>>>> 2 2 0 1
>>>>> 3 0 0 1
>>>>> 3 0 0 1
>>>>> 3 0 0 1
>>>>> 3 0 0 1
>>>>> 3 2 0 1
>>>>> 4 0 1 2
>>>>> 4 0 1 2.
>>>>>
>>>>> Where, COMPL= health complication of diabetic patients which has value
>>>>> labels as 0= no complication,1=coronary heart disease, 2=retinopathy,
>>>>> 3=
>>>>> nephropathy.
>>>>>
>>>>>
>>>>> I want to select only the first complication that occurred to each
>>>>> patient.
>>>>> What R function can I use?
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________**________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>>>>> PLEASE do read the posting guide http://www.R-project.org/**
>>>>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>>>
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>>
>>>> ______________________________**________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>>>> PLEASE do read the posting guide http://www.R-project.org/**
>>>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>>>
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>>
>>>
>>>--
>>>==============================
>>>Xiaogang Su, Ph.D.
>>>Associate Professor & Statistician
>>>School of Nursing, University of Alabama
>>>Birmingham, AL 35294-1210
>>>(205) 934-2355 [Office]
>>>xgsu at uab.edu
>>>xiaogangsu at gmail.com
>>>https://sites.google.com/site/xgsu00/
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>______________________________________________
>>>R-help at r-project.org mailing list
>>>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.
>>>
>>>
>>
>>
>>
>>--
>>==============================
>>Xiaogang Su, Ph.D.
>>Associate Professor & Statistician
>>School of Nursing, University of Alabama
>>Birmingham, AL 35294-1210
>>(205) 934-2355 [Office]
>>xgsu at uab.edu
>>xiaogangsu at gmail.com
>>https://sites.google.com/site/xgsu00/
>
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