Right you are, A.K.
Thanks for catching that.
It should be ...
data2 <- data.frame(
id = rep(data1$ID, 3),
visit = rep(1:3, rep(dim(data1)[1], 3)),
date = as.Date(c(data1$V1Date, data1$V2date, data1$V3date), "%m/%d/%y"),
dva = c(data1$V1a, data1$V2a, data1$V3a),
dvb = c(data1$V1b, data1$V2b, data1$V3b),
dvc = c(data1$V1c, data1$V2c, data1$V3c))
Jean
On Mon, Dec 17, 2012 at 5:08 PM, arun <smartpink...@yahoo.com> wrote:
> Hi Jean,
>
> Just to clarify whether it is a 'typo' or not.
> data2 <- data.frame(
> id = rep(data1$ID, 3),
> visit = rep(1:3, rep(dim(data1)[1], 3)),
> date = as.Date(c(data1$V1Date, data1$V2date, data1$V3date), "%m/%d/%y"),
> dva = c(data1$V1a, data1$V2a, data1$V3a),
> dvb = c(data1$V1a, data1$V2a, data1$V3a),# 'b'
> dvc = c(data1$V1a, data1$V2a, data1$V3a)) # 'c'
>
>
> A.K.
>
>
>
> ----- Original Message -----
> From: "Adams, Jean" <jvad...@usgs.gov>
> To: marcel curlin <marcelcur...@gmail.com>
> Cc: r-help@r-project.org
> Sent: Monday, December 17, 2012 5:29 PM
> Subject: Re: [R] Manipulation of longitudinal data by row
>
> I had some difficulty getting the data read in using the code you included
> in your email, although I'm not sure why. I'm pasting in the code that
> worked for me, below.
>
> I think that the calculations that you want to make would be easier if you
> rearranged your data first. I used your example data to do just that.
> Once the data are rearranged, it is very easy to look at information on
> the last visit from each ID (see code, below). This includes much of the
> information you describe in your query, 1) date of last completed visit 2)
> whether an ID resolved, and 3) what the final pattern was.
>
> Jean
>
> tC <- textConnection("ID V1Date V1a V1b V1c V2date V2a V2b V2c V3date V3a
> V3b V3c
> 001 4/5/12 Yes Yes No 6/18/12 Yes No Yes NA NA NA NA
> 002 1/22/12 No No Yes 7/5/12 Yes No Yes NA NA NA NA
> 003 4/5/12 Yes No No 9/4/12 Yes No Yes 11/1/12 Yes No Yes
> 004 8/18/12 Yes Yes Yes 9/22/12 Yes No Yes NA NA NA NA
> 005 9/6/12 Yes No No NA NA NA NA 12/4/12 Yes No Yes")
> data1 <- read.table(header=TRUE, tC)
> close.connection(tC)
> rm(tC)
>
> # rearrange the data
> data2 <- data.frame(
> id = rep(data1$ID, 3),
> visit = rep(1:3, rep(dim(data1)[1], 3)),
> date = as.Date(c(data1$V1Date, data1$V2date, data1$V3date), "%m/%d/%y"),
> dva = c(data1$V1a, data1$V2a, data1$V3a),
> dvb = c(data1$V1a, data1$V2a, data1$V3a),
> dvc = c(data1$V1a, data1$V2a, data1$V3a))
> # define a new variable that is a combination of the three dichotomous
> variables
> data2$abc <- paste0(substring(data2$dva, 1, 1), substring(data2$dvb, 1, 1),
> substring(data2$dvb, 1, 1))
> # define a new variable that indicates whether the combination is "normal"
> data2$normal <- data2$abc %in% c("YYN", "YNY", "YYN", "NNY")
>
> # eliminate rows without visit information
> data3 <- data2[!is.na(data2$date), ]
> # split the data into lists according to id
> list4 <- split(data3, data3$id)
>
> # show the last visit from each id
> do.call(rbind, lapply(list4, function(df) df[dim(df)[1], ]))
>
>
>
> On Fri, Dec 14, 2012 at 10:37 AM, marcel curlin <marcelcur...@gmail.com
> >wrote:
>
> > I have a dataset of the form below, consisting of one unique ID per
> > row, followed by a series of visit dates. At each visit there are
> > values for 3 dichotomous variables. Of the 8 different possible
> > combinations of the three variables, 4 are "abnormal" and the
> > remaining 4 are "normal". Everyone starts out abnormal, and then
> > either continues to be abnormal at subsequent visits, or resolves to a
> > normal pattern at a later visit (I ignore reversion back to abnormal -
> > once they are normal, they are normal)
> >
> > I have to end up with 4 new columns indicating 1) date of last
> > completed visit (regardless of intervening "NAs", 2) whether an ID
> > resolved or stayed abnormal, 3) if resolved, what the resolution
> > pattern was and 4) what the date of resolution was. NAs always come in
> > groups of 4 (ie no visit date, and no value for the 3 variables) and
> > are ignored.
> >
> > Eventually I have to determine mean time to resolution, mean follow-up
> > time, etc and I think I can do that, but the first part is a bit
> > beyond my coding skill. Suggestions appreciated.
> >
> > tC <- textConnection("
> > ID V1Date V1a V1b V1c V2date V2a V2b V2c V3date V3a V3b V3c
> > 001 4/5/12 Yes Yes No 6/18/12 Yes No Yes NA NA NA NA
> > 002 1/22/12 No No Yes 7/5/12 Yes No Yes NA NA NA NA
> > 003 4/5/12 Yes No No 9/4/12 Yes No Yes 11/1/12 Yes No Yes
> > 004 8/18/12 Yes Yes Yes 9/22/12 Yes No Yes NA NA NA NA
> > 005 9/6/12 Yes No No NA NA NA NA 12/4/12 Yes No Yes
> > ")
> > data1 <- read.table(header=TRUE, tC)
> > close.connection(tC)
> > rm(tC)
> >
> > ______________________________________________
> > 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.
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
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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.
>
>
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