reshape from base vs dcast from reshape2 with missing values

Question

Whis this data frame,

df <- expand.grid(id=\"01\", parameter=c(\"blood\", \"saliva\"), visit=c(\"V1\", \"V2\", \"V3\"))
df$value <- c(1:6)
df$sex <- rep         


        

Answer 1

The relevant part of the reshape code would be the line:

data[, tempidname] <- interaction(data[, idvar], drop = TRUE)

Look at how interaction works:

> interaction("A", "B")
[1] A.B
Levels: A.B
> interaction("A", "B", NA)
[1] <NA>
Levels: 

But, compare what would happen if NA were retained as a level:

> interaction("A", "B", addNA(NA))
[1] A.B.NA
Levels: A.B.NA

Thus, if you want to have the same result with base R's reshape, you need to make sure that any "idvar" columns have NA retained as a level.

Example:

df$sex <- addNA(df$sex)
reshape(df,
        timevar="visit",
        idvar=c("id", "parameter", "sex"),
        direction="wide")
#   id parameter  sex value.V1 value.V2 value.V3
# 1 01     blood <NA>        1       NA       NA
# 2 01    saliva <NA>        2       NA       NA

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Of course, the other question is how NA can be treated as an identifying variable :-)