In the scientific paper "Mapping the Antigenic and Genetic Evolution of Influenza Virus's" Supporting Material, Smith et al write about determining antigenic distance Dij. However, I don't understand how one could calculate Dij from HI values of <10. Is it better to remove these data values or to change it to 9?
Also, regarding the missing data, how does one make a comprehensive antigenic map using shape space distance dij? I see that an error function must be minimized, but how does that give dij for all the missing data? Should missing data be ignored for the error function?