The method is: for a span of a season or more (has been done for at least 30 seasons) you determine how many runs were scored, on average, in each base-out situation (eg, bases empty, no out; runner on first, one out, etc.). The you compare the difference between a single and an out in each of those 24 contexts (eg, for bases empty, no out, you compare the difference between the average number of runs scored with bases empty, one out vs runner on first, no out). Repeat for all 24 contexts. You obviously need to know things like what percentage of runners go first-to-third on a single to get an accurate calculation. Basically, the average difference between average runs scored after a single, and after an out, averaged over all 24 base-out contexts, is 0.73 or so.
The guy who has done the most work with this in the last 15 years is Tom Tango.