I have been trying to run this code (below here) and I have gotten that message \"Error in if (temp[ii] == 0) { : missing value where TRUE/FALSE needed\"...
temp
At a guess I'm going to say that this is in R - if so I'm guessing that this line:
R
if (temp[i] == 0) (or temp[ii] == 0)
is resulting in an NA, and if conditions must have a TRUE or FALSE value.
NA
if
TRUE
FALSE
Using a debugger if you can, I'd interrogate the value of temp[i] before the if block.