Susan:
Your analysis is certainly spot on! There does NOT seem to be room for ALL of both James ROPER's and John ROPER's sons in Jesse ROPER's 1800 Census record, IF Jesse ROPER, Jr., is a son of Jesse ROPER and Thomas ROPER is a son of James ROPER.
Even so, both James ROPER and John ROPER DO seem to fit as individuals with their spouses. While it would be far less common today for parents to syndicate children out to aunts or uncles, with the absence of free public schools, placing a young son in the household of an uncle to learn some additional skills or trade or even placing a daughter in the household of a newly married aunt to give a hand seemed to be a more common solution to both residential space challenges as well as a means of teaching/learning.
While I would certainly concede that it remains far from certain that both John ROPER and James ROPER resided in Jesse ROPER's household, in my view the extant data remains at least generally consistent with that possibility if one slightly relaxes the constraints and admits the possibility that some children might have resided elsewhere.
Jesse ROPER's 1800 household therefore still seems to me to be the single best candidate household to explain the absence of John ROPER and James ROPER from the Census records.
It perhaps bears mention that one other possibility unmentioned in my post in the Thomas ROPER thread is that Thomas ROPER could have also been a son of Jesse ROPER, Jr., if Jesse ROPER was at the upper end of the plausible age range AND Thomas ROPER enlisted for active service BEFORE age 16.
It seems to me that the only really reasonably viable data we have about Thomas ROPER is that he was probably at least age 16 by the date of his militia service (b bef 1799). But even this could possibly be slightly relaxed if one admits the possibility that a boy might lie about his age to serve, possibly with parental complicity.
The known date of John ROPER's marriage and the identification of two children known to have been born before 1800 seems to me to mostly preclude John ROPER as the father, though omission from mention in the HOWELL letter could be readily explained if he died very young. It seems more likely that Jesse ROPER, Jr., married after 1800 and that Thomas ROPER would fit as Jesse ROPER, Jr.'s son only by slightly relaxing the age constraints and assuming that Thomas ROPER went into active service before attaining age 16.
Ascription of Thomas as a son of James ROPER seems to require the fewest other assumptions, EXCEPT possibly for an assumption that one or more of the sons of Jesse, John and/or James wasn't residing in the Jesse ROPER household in 1800. The absent child or children would be least likely to be mere infants (e.g. William F. ROPER) and would probably be of a somewhat productive age where their presence in another household wouldn't be an undue burden and could be mutually rewarding for the child and the family hosting the child.
Occam's Razor teaches us that the simplest explanation for the data is most likely. Based upon evidence identified to date, this would seem to support an ascription of James ROPER as the father.
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I am glad that you noticed the coinciding MEACHAM records! I had remembered seeing MEACHAMs before elsewhere and had made a very cursory search, but hadn't relocated the mentions you now cite.