Selecting First Incidence from Longitudinal Data

2 messages · arun, Frank E Harrell Jr

arun

Sat, Feb 23, 2013 9:45 PM #

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/
>

Frank E Harrell Jr

Sun, Feb 24, 2013 6:51 AM #

I think we need a task view on longitudinal data manipulation.  There are so
many approaches to this - people need help navigating them.

I tend to stay away from the lapply-split methods as they don't look quite
as clean and may take longer to run.  The aggregate function uses too much
data frame subscripting.  The plyr package and the mApply function in the
Hmisc package provide some other nice solutions.  Often I like to stick with
tapply using constructs like 

with(mydata, tapply(1:nrow(mydata), subjectID, function(i) {... operate on
variables in mydata subscripted by [i] ...)))

Frank


arun kirshna wrote

________________________________
From: Tasnuva Tabassum &lt;

head(x[x$COMPL!=0,],1) else head(x,1)))

________________________________
From: Tasnuva Tabassum &lt;

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.

by=list(dat0$ID),FUN=length)$x, FUN=function(x){seq(1, x)})))

by=list(dat1$ID),FUN=length)$x, FUN=function(x){seq(1, x)})))

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 &lt;

xiaogangsu@

&gt;

To: Rui Barradas &lt;

ruipbarradas@

&gt;

Cc:

r-help@

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 &lt;

ruipbarradas@

&gt; 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]]

______________________________**________________

https://stat.ethz.ch/mailman/**listinfo/r-help&lt;https://stat.ethz.ch/mailman/listinfo/r-help&gt;
PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html
&lt;http://www.R-project.org/posting-guide.html&gt;

and provide commented, minimal, self-contained, reproducible code.

______________________________**________________

https://stat.ethz.ch/mailman/**listinfo/r-help&lt;https://stat.ethz.ch/mailman/listinfo/r-help&gt;
PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html &lt;http://www.R-project.org/posting-guide.html&gt;

and provide commented, minimal, self-contained, reproducible code.

______________________________________________

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.

______________________________________________

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.

-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
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