I've been able to come up with this code, it follows my understanding of the problem given your example:
RTdataflat = [1 2 3 NaN 5 6 NaN 8 9 NaN];
outcomeflat = [3 4 7 NaN 9 2 8 9];
%Define your vectors
[Rx,Ry] = size(RTdataflat);
[ox,oy] = size(outcomeflat);
%Gets sizes of the vectors
q =Ry-oy;
outcomeflat(end+q) = 0;
%Pre-allocates some extra space in outcomeflat for the NaN variables
for b = 1:Ry
if isnan(RTdataflat(Rx,b))
if ~isnan(outcomeflat(Rx,b))
for c = flip(b:Ry)
outcomeflat(1,c) = outcomeflat(1,c-1); %Moves all data to allow space for NaN if data does not contain NaN already
end
end
outcomeflat(Rx,b) = NaN; %Adds NaN into the vector
end
end
%Returns the vector [3,4,7,NaN,9,2,NaN,8,9,NaN] as requested.
