[R] Advice on recoding a variable depending on another which contains NAs

[Anthony Staines]

Dear colleagues,

I would be very grateful for your help with the following. I 
have banged my head off this question several times in the 
past, and repeatedly over the last week. I have looked in 
the usual places and found no obvious solution. I fear that 
this just means I didn't recognize it, but I'd be very 
grateful for your help.

I am scoring 8000 psychometric tests - the SCQ, if you have 
heard of it. On this test the scoring rules depends on one 
variable SCQ1 - if this is answered yes, the final score is 
a function of 39 variables, and if no, of 31 variables.

I've calculated both of these scores (SCQScore1 and 
SCQScore2)for all the children in my study, and I wish to 
create a final score, which is SCQScore1 when SCQ1 is 1, and 
SCQScore2 when SCQ1 is 2. There are also missing values for 
SCQ1, and I have chosen, for the moment, to set the final 
score to SCQScore1 for these. [[This is a debatable choice, 
but I am not asking your advice on that choice!]]

d$SCQScore <- 99
	##Distinct value for any other values I've missed

d$SCQScore[SCQ1 == 1] <- d$SCQScore1[SCQ1 == 1]
	## Talks using phrases/sentences, so sum S2CQ:SCQ40

d$SCQScore[SCQ1 == 2] <- d$SCQScore2[SCQ1 == 2]
	## Can't do this, so sum SCQ8:SCQ40

d$SCQScore[is.na(d$SCQ1)] <- d$SCQScore1 [is.na(d$SCQ1)]
	## SCQ1 is missing

This fails on line 2
(d$SCQScore[SCQ1 == 1] <- d$SCQScore1[SCQ1 == 1])
  with the error message
"NAs are not allowed in subscripted assignments",
presumably because SCQ1 does indeed contain missing values.

This can be fixed, got around, or otherwise bypassed, by 
creating a new variable SCQ1, with no missing values, as 
shown :-

SCQ1 <- d$SCQ1
SCQ1[is.na(SCQ1)] <- 3

d$SCQScore[SCQ1 == 1] <- d$SCQScore1[SCQ1 == 1]
	## Talks using phrases/sentences so sum S2CQ:SCQ40
d$SCQScore[SCQ1 == 2] <- d$SCQScore2[SCQ1 == 2]
	## Can't do this, so sum SCQ8:SCQ40
d$SCQScore[SCQ1 == 3] <- d$SCQScore1[SCQ1 == 3]
	## We don't know if he/she can talk, so guess - sum S2:S40

This type of thing is a common problem in my little world. 
Is there a better/less klutzy/smarter way of solving it than 
creating a new variable each time? Please bear in mind that 
it is critical, for later analysis, to keep the missing 
values in SCQ1.

Best wishes,
Anthony Staines
-- 
Anthony Staines, Professor of Health Systems,
School of Nursing and Human Sciences, DCU, Dublin 9,Ireland.
Tel:- +353 1 700 7807. Mobile:- +353 86 606 9713
http://astaines.eu/