I think this is what you are looking for. The line with the variable 'con' is not really necessary, but if you need to reference the connections later it would be convenient.
R=0.3; %%radius
n = input('Enter number of nodes: ');
d=zeros(n,n);
con=zeros(n,n); % matrix of zeros indicates none are connected
x = rand(1,n);
y = rand(1,n);
plot(x,y,'o');
hold on
for i = 1 : (n)
for j = 1 : (n)
d(i, j) = sqrt((x(i) - x(j)) ^ 2 + (y(i) - y(j)) ^ 2);
if (d(i,j)<R)
con(i,j)=1; % sets to 1 to indicate connection between node i and j
hold on
line([x(i), x(j)],[y(i), y(j)]);
end
end
end
