Transfer pivottable to another table in R - r

Question

In my research I have a dataset of cancer patients with some clinical information like cancer stage and treatment etc. Each patient has one row in a table with this clinical information. In addition, each patient has, at one or several timepoints during the treatment, taken blood samples, depending on how long the patient has been followed at the clinic. The first sample is from the first visit and the second sample is from the second visit at the clinic, and so on.
In the table, there is a variable (ie. column) that is named Sample_Time_1, which is the time for the first sample. Sample_Time_2 has the time (date) for the second sample and so on.
However - the samples were analysed at the lab and I got the result in a pivottable, which means I have a table where each sample has one row and therefore the results from one patient is displayed on several rows.
For example, create two tables:
x <- c(1,2,2,3,3,3,3,4,5,6,6,6,6,7,8,9,9,10)
y <- as.Date(c("2011-05-17","2012-06-30","2012-08-11","2011-10-15","2011-11-25","2012-01-07","2012-02-15","2011-08-13","2012-02-03","2011-11-08","2011-12-21","2012-02-01","2012-03-12","2012-01-03","2012-04-20","2012-03-31","2012-05-10","2011-12-15"), format="%Y-%m-%d", origin="1960-01-01")
z <- c(123,185,153,153,125,148,168,187,194,115,165,167,143,151,129,130,151,134)
Sheet_1 <- matrix(c(x,y,z), ncol=3, byrow=FALSE)
colnames(Sheet_1) <- c("ID","Sample_Time", "Sample_Value")
Sheet_1 <- as.data.frame(Sheet_1)
Sheet_1$Sample_Time <- y
x1 <- c(1,2,3,4,5,6,7,8,9,10)
x2 <- c(3,3,2,3,2,2,4,2,3,3)
x3 <- c(1,2,2,3,3,1,3,1,1,2)
x4 <- as.Date(c("2011-05-17","2012-06-30","2011-10-15","2011-08-13","2012-02-03","2011-11-08","2012-01-03","2012-04-20","2012-03-31","2011-12-15"), format="%Y-%m-%d", origin="1960-01-01")
x5 <- as.Date(c(NA,"2012-08-11","2011-11-25",NA,NA,"2011-12-21",NA,NA,"2012-05-10",NA), format="%Y-%m-%d", origin="1960-01-01")
x6 <- as.Date(c(NA,NA,"2012-01-07",NA,NA,"2012-02-01",NA,NA,NA,NA), format="%Y-%m-%d", origin="1960-01-01")
x7 <- as.Date(c(NA,NA,"2012-02-15",NA,NA,"2012-03-12",NA,NA,NA,NA), format="%Y-%m-%d", origin="1960-01-01")
Sheet_2 <- as.data.frame(c(1:10))
colnames(Sheet_2) <- "ID"
Sheet_2$Stage <- x2
Sheet_2$Treatment <- x3
Sheet_2$Sample_Time_1 <- x4
Sheet_2$Sample_Time_2 <- x5
Sheet_2$Sample_Time_3 <- x6
Sheet_2$Sample_Time_4 <- x7
Sheet_2$Sample_Value_1 <- NA
Sheet_2$Sample_Value_2 <- NA
Sheet_2$Sample_Value_3 <- NA
Sheet_2$Sample_Value_4 <- NA
I would like to transfer the Sample_Value for the first date a sample was taken from a patient from Sheet_1 to Sheet_2$Sample_Value_1 and if there are more samples, I would like to transfer them to column "Sample_Value_2" and so on.
I have tried with a double for-loop. For each patient (=ID) in Sheet_1 I have run through Sheet_2 and if there is a mach on ID, then I use another for-loop to see if there is a mach on a Sample_Time and insert (using if) the Sample_Value. However, I do not manage to get it to work and I have a strong feeling there must be a better way.
Any suggestions?

Answer 1

Is this what you want:
Prepare Sheet_1 for reshaping from long to wide by introducing an extra column with unique ID for each blood sample per patient
Sheet_1$uniqid <- with(Sheet_1, ave(as.character(ID), ID, FUN = seq_along))
And with this, do the re-shaping
S_1 <- reshape( Sheet_1, idvar = "ID", timevar = "uniqid", direction = "wide")
which gives you
> S_1
ID Sample_Time.1 Sample_Value.1 Sample_Time.2 Sample_Value.2 Sample_Time.3
1 1 2011-05-17 123 <NA> NA <NA>
2 2 2012-06-30 185 2012-08-11 153 <NA>
4 3 2011-10-15 153 2011-11-25 125 2012-01-07
8 4 2011-08-13 187 <NA> NA <NA>
9 5 2012-02-03 194 <NA> NA <NA>
10 6 2011-11-08 115 2011-12-21 165 2012-02-01
14 7 2012-01-03 151 <NA> NA <NA>
15 8 2012-04-20 129 <NA> NA <NA>
16 9 2012-03-31 130 2012-05-10 151 <NA>
18 10 2011-12-15 134 <NA> NA <NA>
Sample_Value.3 Sample_Time.4 Sample_Value.4
1 NA <NA> NA
2 NA <NA> NA
4 148 2012-02-15 168
8 NA <NA> NA
9 NA <NA> NA
10 167 2012-03-12 143
14 NA <NA> NA
15 NA <NA> NA
16 NA <NA> NA
18 NA <NA> NA
The number after the dot in the colnames is the uniqid.
Now you can merge the relevant columns from Sheet_2
S_2 <- merge( Sheet_2[ 1:3 ], S_1, by = "ID" )
and the result should be what you are looking for:
> S_2
ID Stage Treatment Sample_Time.1 Sample_Value.1 Sample_Time.2 Sample_Value.2
1 1 3 1 2011-05-17 123 <NA> NA
2 2 3 2 2012-06-30 185 2012-08-11 153
3 3 2 2 2011-10-15 153 2011-11-25 125
4 4 3 3 2011-08-13 187 <NA> NA
5 5 2 3 2012-02-03 194 <NA> NA
6 6 2 1 2011-11-08 115 2011-12-21 165
7 7 4 3 2012-01-03 151 <NA> NA
8 8 2 1 2012-04-20 129 <NA> NA
9 9 3 1 2012-03-31 130 2012-05-10 151
10 10 3 2 2011-12-15 134 <NA> NA
Sample_Time.3 Sample_Value.3 Sample_Time.4 Sample_Value.4
1 <NA> NA <NA> NA
2 <NA> NA <NA> NA
3 2012-01-07 148 2012-02-15 168
4 <NA> NA <NA> NA
5 <NA> NA <NA> NA
6 2012-02-01 167 2012-03-12 143
7 <NA> NA <NA> NA
8 <NA> NA <NA> NA
9 <NA> NA <NA> NA
10 <NA> NA <NA> NA