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.
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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