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I'm looking at the footnotes in John Jewel's ''Defence of the Apology of the Church of England'' and I see this abbreviation repeated in many citations:

Marcellin. Condemn. in eod. Tom. I. p. 192, 4, 6, 7; where unus autem de episcopis nomine Quirinus, and et moram eum.

Innoc. III. in eod. Decretal. Gregor. IX. Lib. III. Tit. xlii. cap. 3. cols. 1386, &c.

What does this abbreviation mean?

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I haven't actually seen that abbreviation before, but I would guess that that's short for in eōdem: "in the same [place]". In is the preposition "in", while eōdem is (ablative of id "it") + -dem (combines with id to form idem "same").

(L&S do seem to have a note about this abbreviation in particular, under the entry eodem. Unfortunately, Perseus is down, so I can't actually read it.)

2

Ibid. short for Ibidem, 'in the same place' is the usual term for 'from the same source.'
But it may be that "in eodem" also means 'in the same book, source.'

For 'ibid.' see footnotes p 353, The Defence of the Apology, giving (3)further references to Gratian as a source. This is the usual usage.
p. 158 footnote 6 [Id. /idem/ ad deuter. Epist. ccxxxvi.2.Tom. II. col. 848.]

However, 'in eodem' and 'ibid.' appear on the same footnote on p.203 note10

[ ..neminem potest iniqua gravare sententia- Gelas. in eodem ibid. Caus. xi. Quaest. iii. can. 47. col 938.]

And from the examples and lexical references so far shown it is possible that in eodem means "upon the same rationale," "upon the same grounds."

Ainsworth: 1783
in, +ABLAT. (20) Concerning. (example for 20) Idem in servo dici solet,
The same can be said in respect of, with regard to, a slave.

Similar examples can be found in Lewis and Short: In +Ablative. 'On the subject of..'

The footnotes would then be drawing attention to other examples of the same argument, the same style of reasoning, the same principle, rather than quotations from the same book.

Yet it must be said that there is no reference to 'in eodem' as a set phrase in:
Smith: 'in,' 'idem,' 'eodem.'
Lewis and Short: 'in,' 'idem,' 'eodem.'
Ainsworth: 'in,' 'idem,' 'eodem.'
Prefaces to all these lexicons, and to English dictionaries.

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