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Unrolled code and explanation :

function(v){          # v vector of tunnel indexes (1-based) or values <= 0

  a = v[v>0]          # get the tunnel positions

  b = sort(a)         # sort the tunnel positions ascending

  c1 = v[a]==b        # get the values of 'v' at positions 'a'
                      # and check if they're equal to the sorted positions 'b'
                      # (element-wise, returns a vector of TRUE/FALSE)

  c2 = a != b         # check if positions 'a' are different from sorted positions 'b' 
                      # (to exclude tunnels pointing to themselves, element-wise,
                      #  returns a vector of TRUE/FALSE)

  all(c1 & c2)        # if all logical conditions 'c1' and 'c2' are TRUE then
                      # returns TRUE otherwise FALSE