On Wed, Dec 7, 2011 at 4:02 AM, Eric Fail <eric.f...@gmx.us> wrote:
> Dear list,
>
> I have been struggling with this for some time now, and for the last hour I
> have been struggling to make a working example for the list. I hope someone
> out there have some experience with plotting longitudinal data that they will
> share.
>
> My data is some patient data with three different time stamps. First the
> patients are identified at different times (first time stamp). Second, they
> go through an assessment phase and begin their treatment (time stamp 2).
> Finally they are admitted from the hospital at some point (time stamp 3),
>
> I would like to make a spaghetti plot with the assessment phase in one color
> and the treatment phase in another color.
>
> I used ggplot2, and with this example data and only two time points; it works
> fine (I call it my working example),
>
> library(ggplot2)
> df <- data.frame(
> date = seq(Sys.Date(), len=104, by="1 day")[sample(104, 52)],
> patient = factor(rep(1:26, 2), labels = LETTERS)
> )
> df <- df[order(df$date), ]
> dt <- qplot(date, patient, data=df, geom="line")
> dt + scale_x_date()
> df[ which(df$patient=='E'), c("patient", "date")]
>
> But, if I have three time points, R, for some reason I do not yet understand,
> add the two second time points in some funny way.
>
> Finally, when that is solved; how do I colorize the different parts of the
> line so the assessment phase gets one color and the treatment phase another?
>
> I want to be able to show how long we have been in contact with our patients,
> how much of the contact time that was assessment and how much that was actual
> treatment.
>
> Below is an example (I call it the not-working example)
>
> df2 <- data.frame(
> date2 = seq(Sys.Date(), len= 156, by="2 day")[sample(156, 78)],
> patient2 = factor(rep(1:26, 3), labels = LETTERS)
> )
>
> df2 <- df2[order(df2$date2), ]
> dt2 <- qplot(date2, patient2, data=df2, geom="line")
> dt2 + scale_x_date(major="months", minor="weeks")
> df2[ which(df2$patient2=='B'), c("patient2", "date2")]
Did you mean something like this?
library(ggplot2)
library(plyr)
df2 <- data.frame(
date2 = seq(Sys.Date(), len= 156, by="2 day")[sample(156, 78)],
patient2 = factor(rep(1:26, 3), labels = LETTERS)
)
df2 <- ddply(df2, "patient2", mutate, visit = order(date2))
qplot(date2, patient2, data = df2, geom = "line") +
geom_point(aes(colour = factor(visit)))
# or this?
library(ggplot2)
library(plyr)
df2 <- data.frame(
date2 = seq(Sys.Date(), len= 156, by="2 day")[sample(156, 78)],
patient2 = factor(rep(1:26, 3), labels = LETTERS)
)
df2 <- ddply(df2, "patient2", mutate, visit = order(date2))
qplot(date2, patient2, data = df2, geom = "line", colour =
factor(visit), group = patient2)
# Obviously the lines are drawn between the observations so you only
see the first two visits.
Hadley
--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/
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