Re: [R] Selecting First Incidence from Longitudinal Data
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
> 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$COMPL!=0,],1) else head(x,1)))
> # ID COMPL SEX HEREDITY
> #1 1 3 1 2
> #2 2 1 0 1
> #3 3 2 0 1
> #4 4 0 1 2
>
>
> You could also try:
> dat1[with(dat1,ave(COMPL,ID,FUN=function(x) if(any(x!=0)) cumsum(x>0) else
> seq_along(x)))==1,] #modification of David's code
> # ID COMPL SEX HEREDITY
> #3 1 3 1 2
> #5 2 1 0 1
> #12 3 2 0 1
> #13 4 0 1 2
> A.K.
>
>
>
>
>
> ________
> From: Tasnuva Tabassum <
> t.tasnuva@
> >
> To: arun <
> smartpink111@
> >
> Sent: Sunday, February 24, 2013 12:08 AM
> Subject: Re: [R] Selecting First Incidence from Longitudinal Data
>
>
> sorry, I tried this. But it gave me answer:
>
> # ID COMPL SEX HEREDITY
> #1 1 0 1 2
> #4 2 0 0 1
> #8 3 0 0 1
> #13 4 0 1 2
>
>
>
>
> On Sat, Feb 23, 2013 at 8:44 PM, arun <
> smartpink111@
> > wrote:
>
> Hi,
>>Try this:
>>#dat1
>> do.call(rbind,lapply(split(dat1,dat1$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@
> >
>>To: Xiaogang Su <
> xiaogangsu@
> >
>>Cc: arun <
> smartpink111@
> >; R help <
> r-help@
> >; Rui Barradas <
> ruipbarradas@
> >
>>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@
> > 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@
> > wrote:
>>>
>>>HI,
>>>>Tried your approach:
&g
Re: [R] Selecting First Incidence from Longitudinal Data
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$COMPL!=0,],1) else head(x,1)))
# ID COMPL SEX HEREDITY
#1 1 3 1 2
#2 2 1 0 1
#3 3 2 0 1
#4 4 0 1 2
You could also try:
dat1[with(dat1,ave(COMPL,ID,FUN=function(x) if(any(x!=0)) cumsum(x>0) else
seq_along(x)))==1,] #modification of David's code
# ID COMPL SEX HEREDITY
#3 1 3 1 2
#5 2 1 0 1
#12 3 2 0 1
#13 4 0 1 2
A.K.
From: Tasnuva Tabassum
To: arun
Sent: Sunday, February 24, 2013 12:08 AM
Subject: Re: [R] Selecting First Incidence from Longitudinal Data
sorry, I tried this. But it gave me answer:
# ID COMPL SEX HEREDITY
#1 1 0 1 2
#4 2 0 0 1
#8 3 0 0 1
#13 4 0 1 2
On Sat, Feb 23, 2013 at 8:44 PM, arun wrote:
Hi,
>Try this:
>#dat1
> do.call(rbind,lapply(split(dat1,dat1$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
>To: Xiaogang Su
>Cc: arun ; R help ; Rui Barradas
>
>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 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 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$sequence==1,] #here the OP wanted first incidence where COMPL!=0
>>># ID COMPL SEX HEREDITY sequence
>>>#1 1 0 1 2 1
>>>#4 2 0 0 1 1
>>>#8 3 0 0 1 1
>>>#13 4 0 1 2 1
>>>A.K.
>>>
>>>
>>>
>>>
>>>- Original Message -
>>>From: Xiaogang Su
>>>To: Rui Barradas
>>>Cc: r-help@r-project.org
>>>Sent: Saturday, February 23, 2013 2:15 PM
>>>Subject: Re: [R] Selecting First Incidence from Longitudinal Data
>>>
>>>Try this:
>>>dat$sequence <- as.vector(unlist(lapply( aggregate(dat$ID, by=list(x),
>>>FUN=length)$x, FUN=function(x){seq(1, x
>>>dat0 <- dat[dat$sequence==1, ]
>>>
>>>HTH, X
>>>
>>>
>>>On Sat, Feb 23, 2013 at 1:07 PM, Rui Barradas wrote:
>>>
>>>> Hello,
>>>>
>>>> You can use ?aggregate an
Re: [R] Selecting First Incidence from Longitudinal Data
Hi,
Try this:
#dat1
do.call(rbind,lapply(split(dat1,dat1$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
To: Xiaogang Su
Cc: arun ; R help ; Rui Barradas
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 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 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$sequence==1,] #here the OP wanted first incidence where COMPL!=0
>># ID COMPL SEX HEREDITY sequence
>>#1 1 0 1 2 1
>>#4 2 0 0 1 1
>>#8 3 0 0 1 1
>>#13 4 0 1 2 1
>>A.K.
>>
>>
>>
>>
>>- Original Message -
>>From: Xiaogang Su
>>To: Rui Barradas
>>Cc: r-help@r-project.org
>>Sent: Saturday, February 23, 2013 2:15 PM
>>Subject: Re: [R] Selecting First Incidence from Longitudinal Data
>>
>>Try this:
>>dat$sequence <- as.vector(unlist(lapply( aggregate(dat$ID, by=list(x),
>>FUN=length)$x, FUN=function(x){seq(1, x
>>dat0 <- dat[dat$sequence==1, ]
>>
>>HTH, X
>>
>>
>>On Sat, Feb 23, 2013 at 1:07 PM, Rui Barradas wrote:
>>
>>> Hello,
>>>
>>> You can use ?aggregate and ?head to do what you want. Try the following.
>>>
>>>
>>>
>>> dat <- read.table(text="
>>>
>>> ID COMPL SEX HEREDITY
>>> 1 0 1 2
>>> 1 0 1 2
>>> 1 3 1 2
>>> 2 0 0 1
>>> 2 1 0 1
>>> 2 2 0 1
>>> 2 2 0 1
>>> 3 0 0 1
>>> 3 0 0 1
>>> 3 0 0 1
>>> 3 0 0 1
>>> 3 2 0 1
>>> 4 0 1 2
>>> 4 0 1 2
>>> ", header = TRUE)
>>>
>>> aggregate(. ~ ID, data = subset(dat, COMPL != 0), head, 1)
>>>
>>>
>>> Hope this helps,
>>>
>>> Rui Barradas
>>>
>>> Em 23-02-2013 14:28, Tasnuva Tabassum escreveu:
>>>
>>> I have a longitudinal competing risk data of the form:
>>>>
>>>> ID COMPL SEX HEREDITY
>>>> 1 0 1 2
>>>> 1 0 1 2
>>>> 1 3 1 2
>>>> 2 0 0 1
>>>> 2 1 0 1
>>>> 2 2 0 1
>>>> 2 2 0 1
>>>> 3 0 0 1
>>>> 3 0 0 1
>>>> 3 0 0 1
>>>> 3 0 0 1
>>>> 3 2 0 1
>>>> 4 0 1 2
>>>> 4 0 1 2.
>>>>
>>>> Where, COMPL= health complication of diabetic patients which has value
>>>> labels as 0= no complication,1=coronary heart disease, 2=retinopathy,
>>>> 3=
>>>> nephropathy.
>>>>
>>>>
Re: [R] Selecting First Incidence from Longitudinal Data
Hi
Thank you very much, but I forgot to tell that I also want to include the
patients for which no complication occurred. That is, for my data I want to
include patient no. 4, for which the COMPL value will be 0.
In that case, what R function should I write?
On Sat, Feb 23, 2013 at 12:23 PM, Xiaogang Su wrote:
> My bad. I didn't try it out with the real data. Here you go. HTH, X
>
> dat <- read.table(text="
> IDCOMPL SEX HEREDITY
> 10 1 2
> 10 1 2
> 13 1 2
> 20 0 1
> 21 0 1
> 22 0 1
> 22 0 1
> 30 0 1
> 30 0 1
> 30 0 1
> 30 0 1
> 32 0 1
> 40 1 2
> 40 1 2
> ", header = TRUE)
>
> dat0 <- dat[dat$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$sequence==1, ]
> dat0
>
>
>
> On Sat, Feb 23, 2013 at 2:09 PM, arun wrote:
>
>> HI,
>> Tried your approach:
>>
>>
>> dat1$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$COMPL!= 0, ] #your second solution
>> dat0
>> #[1] ID COMPLSEX HEREDITY sequence
>> #<0 rows> (or 0-length row.names)
>>
>>
>> dat1[dat1$sequence==1,] #here the OP wanted first incidence where COMPL!=0
>> # ID COMPL SEX HEREDITY sequence
>> #1 1 0 121
>> #4 2 0 011
>> #8 3 0 0 1 1
>> #13 4 0 1 2 1
>> A.K.
>>
>>
>>
>> - Original Message -
>> From: Xiaogang Su
>> To: Rui Barradas
>> Cc: r-help@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
>> wrote:
>>
>> > Hello,
>> >
>> > You can use ?aggregate and ?head to do what you want. Try the following.
>> >
>> >
>> >
>> > dat <- read.table(text="
>> >
>> > IDCOMPL SEX HEREDITY
>> > 10 1 2
>> > 10 1 2
>> > 13 1 2
>> > 20 0 1
>> > 21 0 1
>> > 22 0 1
>> > 22 0 1
>> > 30 0 1
>> > 30 0 1
>> > 30 0 1
>> > 30 0 1
>> > 32 0 1
>> > 40 1 2
>> > 40 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:
>> >>
>> >> IDCOMPL 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@r-project.
Re: [R] Selecting First Incidence from Longitudinal Data
My bad. I didn't try it out with the real data. Here you go. HTH, X
dat <- read.table(text="
IDCOMPL SEX HEREDITY
10 1 2
10 1 2
13 1 2
20 0 1
21 0 1
22 0 1
22 0 1
30 0 1
30 0 1
30 0 1
30 0 1
32 0 1
40 1 2
40 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 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 COMPLSEX HEREDITY sequence
> #<0 rows> (or 0-length row.names)
>
>
> dat1[dat1$sequence==1,] #here the OP wanted first incidence where COMPL!=0
> # ID COMPL SEX HEREDITY sequence
> #1 1 0 121
> #4 2 0 011
> #8 3 0 011
> #13 4 0 121
> A.K.
>
>
>
> - Original Message -
> From: Xiaogang Su
> To: Rui Barradas
> Cc: r-help@r-project.org
> Sent: Saturday, February 23, 2013 2:15 PM
> Subject: Re: [R] Selecting First Incidence from Longitudinal Data
>
> Try this:
> dat$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
> wrote:
>
> > Hello,
> >
> > You can use ?aggregate and ?head to do what you want. Try the following.
> >
> >
> >
> > dat <- read.table(text="
> >
> > IDCOMPL SEX HEREDITY
> > 10 1 2
> > 10 1 2
> > 13 1 2
> > 20 0 1
> > 21 0 1
> > 22 0 1
> > 22 0 1
> > 30 0 1
> > 30 0 1
> > 30 0 1
> > 30 0 1
> > 32 0 1
> > 40 1 2
> > 40 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:
> >>
> >> IDCOMPL 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@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@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.
> >
>
>
>
> --
> ==
> X
Re: [R] Selecting First Incidence from Longitudinal Data
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
To: Rui Barradas
Cc: r-help@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 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@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@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]
x...@uab.edu
xiaogan...@gmail.com
https://sites.google.com/site/xgsu00/
[[alternative HTML version deleted]]
__
R-help@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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Selecting First Incidence from Longitudinal Data
To account for COMP,
dat$sequence <- as.vector(unlist(lapply( aggregate(dat$ID, by=list(dat$ID),
FUN=length)$x, FUN=function(x){seq(1, x
dat0 <- dat[dat$sequence==1 & dat$COMPL!= 0, ]
HTH, X
On Sat, Feb 23, 2013 at 1:15 PM, Xiaogang Su wrote:
> 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 wrote:
>
>> Hello,
>>
>> You can use ?aggregate and ?head to do what you want. Try the following.
>>
>>
>>
>> dat <- read.table(text="
>>
>> IDCOMPL SEX HEREDITY
>> 10 1 2
>> 10 1 2
>> 13 1 2
>> 20 0 1
>> 21 0 1
>> 22 0 1
>> 22 0 1
>> 30 0 1
>> 30 0 1
>> 30 0 1
>> 30 0 1
>> 32 0 1
>> 40 1 2
>> 40 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:
>>>
>>> IDCOMPL 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@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.
>>>
>>>
>> __**
>> R-help@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]
> x...@uab.edu
> xiaogan...@gmail.com
> https://sites.google.com/site/xgsu00/
--
==
Xiaogang Su, Ph.D.
Associate Professor & Statistician
School of Nursing, University of Alabama
Birmingham, AL 35294-1210
(205) 934-2355 [Office]
x...@uab.edu
xiaogan...@gmail.com
https://sites.google.com/site/xgsu00/
[[alternative HTML version deleted]]
__
R-help@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.
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 wrote:
> Hello,
>
> You can use ?aggregate and ?head to do what you want. Try the following.
>
>
>
> dat <- read.table(text="
>
> IDCOMPL SEX HEREDITY
> 10 1 2
> 10 1 2
> 13 1 2
> 20 0 1
> 21 0 1
> 22 0 1
> 22 0 1
> 30 0 1
> 30 0 1
> 30 0 1
> 30 0 1
> 32 0 1
> 40 1 2
> 40 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:
>>
>> IDCOMPL 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@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.
>>
>>
> __**
> R-help@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]
x...@uab.edu
xiaogan...@gmail.com
https://sites.google.com/site/xgsu00/
[[alternative HTML version deleted]]
__
R-help@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.
Re: [R] Selecting First Incidence from Longitudinal Data
Hello, You can use ?aggregate and ?head to do what you want. Try the following. dat <- read.table(text=" IDCOMPL SEX HEREDITY 10 1 2 10 1 2 13 1 2 20 0 1 21 0 1 22 0 1 22 0 1 30 0 1 30 0 1 30 0 1 30 0 1 32 0 1 40 1 2 40 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: IDCOMPL 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@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. __ R-help@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.
Re: [R] Selecting First Incidence from Longitudinal Data
Hi, You can also use: do.call(rbind,lapply(split(dat1,dat1$ID),function(x) head(x[x$COMPL!=0,],1))) # ID COMPL SEX HEREDITY #1 1 3 1 2 #2 2 1 0 1 #3 3 2 0 1 - Original Message - From: Tasnuva Tabassum To: r-help@r-project.org Cc: Sent: Saturday, February 23, 2013 9:28 AM Subject: [R] Selecting First Incidence from Longitudinal Data 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@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. __ R-help@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.
Re: [R] Selecting First Incidence from Longitudinal Data
On Feb 23, 2013, at 6:28 AM, Tasnuva Tabassum wrote: > I have a longitudinal competing risk data of the form: > > IDCOMPL 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? > > dat[ with(dat, ave(COMPL, ID, FUN=function(x) cumsum(x>0) ) ) ==1,] ID COMPL SEX HEREDITY 3 1 3 12 5 2 1 01 12 3 2 01 > [[alternative HTML version deleted]] > > __ > R-help@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. David Winsemius Alameda, CA, USA __ R-help@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.
Re: [R] Selecting First Incidence from Longitudinal Data
Hi, Try this: 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) library(plyr) dat2<- dat1[ddply(dat1,.(ID),summarise,COMPL!=0)[,2],] aggregate(.~ID,data=dat2,head,1) # ID COMPL SEX HEREDITY #1 1 3 1 2 #2 2 1 0 1 #3 3 2 0 1 A.K. - Original Message - From: Tasnuva Tabassum To: r-help@r-project.org Cc: Sent: Saturday, February 23, 2013 9:28 AM Subject: [R] Selecting First Incidence from Longitudinal Data 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@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. __ R-help@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.
