I don't know this Numista rarity index at all, but from what I can see it appears that the higher the number, the rarer the item. I was initially thrown by the R7, because the grading scale used by ESC (for example) only goes up to 7 which means extremely rare. Freeman goes up to 20 which is ‘possibly unique’. With your (fairly standard) Charles II 4d rated R40, I deduce that index may go up to 100?
ETA: just Googled, and indeed it goes up to 100, but they say it’s based on how many Numista members have the item and how often it is up for ‘swap’, so fairly esoteric, I'd say!