On 24/06/2009, at 9:52 AM, Alan Cohen wrote:
Hi all,
I am trying to convert a data set of physician death codings (each
individual's cause of death is coded by multiple physicians) from
long to wide format, but the "reshape" function doesn't seem to
work because it requires a "time" variable to identify the sequence
among the repeated observations within individuals. My data set
has no order, and different numbers of physicians code each death,
up to 23. It is also quite large, so for-loops are very slow, and
I'll need to repeat the procedure multiple times. So I'm looking
for a processor-efficient way to replicate "reshape" without a time
variable.
Basically your data ***should*** have a ``time variable''. To me
it looks perilous not to have one. Since you haven't got one, create
one:
make.time <- function(a) {
u <- tapply(1:length(a),a,function(x){
y <- 1:length(x)
names(y) <- x
y}
)
v <- unlist(u)
w <- as.numeric(unlist(lapply(u,names)))
z <- numeric(length(a))
z[w] <- v
z}
Now try the following:
id <- rep(1:5,2)
COD <- c("A01","A02","A03","A04","A05","B01","A02","B03","B04","A05")
MDid <- c(1:6,3,5,7,2)
data <- as.data.frame(cbind(id,COD,MDid))
data$time <- make.time(data$id)
wide <- reshape(data,timevar="time",v.names=c
("COD","MDid"),direction="wide")
Except for the order of the columns (which you can easily rearrange
if it matters,
which it doesn't) the result appears to be what you want.
cheers,
Rolf Turner
Thanks in advance for any help you can provide. A worked example
and some code I've tried are below. I'm working with R v2.8.1 on
Windows XP Professional.
Cheers,
Alan Cohen
Here's what my data look like now:
id <- rep(1:5,2)
COD <- c("A01","A02","A03","A04","A05","B01","A02","B03","B04","A05")
MDid <- c(1:6,3,5,7,2)
data <- as.data.frame(cbind(id,COD,MDid))
data
id COD MDid
1 1 A01 1
2 2 A02 2
3 3 A03 3
4 4 A04 4
5 5 A05 5
6 1 B01 6
7 2 A02 3
8 3 B03 5
9 4 B04 7
10 5 A05 2
And here's what I'd like them to look like:
id2 <- 1:5
COD.1 <- c("A01","A02","A03","A04","A05")
COD.2 <- c("B01","A02","B03","B04","A05")
MDid.1 <- 1:5
MDid.2 <-c(6,3,5,7,2)
data.wide <- as.data.frame(cbind(id2,COD.1,COD.2,MDid.1,MDid.2))
data.wide
id2 COD.1 COD.2 MDid.1 MDid.2
1 1 A01 B01 1 6
2 2 A02 A02 2 3
3 3 A03 B03 3 5
4 4 A04 B04 4 7
5 5 A05 A05 5 2
Here's the for-loop that's very slow (with or without the if-
clauses activated):
ids<-unique(data$id)
ct<-length(ids)
codes<-matrix(0,ct,11)
colnames(codes)<-c
("ID","ICD1","Coder1","ICD2","Coder2","ICD3","Coder3","ICD4","Coder4",
"ICD5","Coder5")
j<-0
for (i in 1:ct){
kkk <- ids[i]
rpt<-data[data$id==kkk,]
j<-max(j,nrow(rpt))
codes[i,1]<-kkk
codes[i,2]<-rpt$ICDCode[1]
codes[i,3]<-rpt$T_Physician_ID[1]
#if (nrow(rpt)>=2){
codes[i,4]<-rpt$ICDCode[2]
codes[i,5]<-rpt$T_Physician_ID[2]
#if (nrow(rpt)>=3) {
codes[i,6]<-rpt$ICDCode[3]
codes[i,7]<-rpt$T_Physician_ID[3]
#if (nrow(rpt)>=4) {
codes[i,8]<-rpt$ICDCode[4]
codes[i,9]<-rpt$T_Physician_ID[4]
#if (nrow(rpt)>=5) {
codes[i,10]<-rpt$ICDCode[5]
codes[i,11]<-rpt$T_Physician_ID[5]
#}}}}
}
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and provide commented, minimal, self-contained, reproducible code.
