The journals may be found in ADM 101 series. Doing a search on 'Nelson' provided the following:
ADM 101/123/2B Medical journal of HMS Theseus for 26 May to 18 August 1797 by Thomas Eshelby, Surgeon, during which time the said ship was employed off Cadiz. Folios 7, 9 - 12, 14- 16: Admiral Horatio Nelson; disease or hurt, compound fracture of the right arm by a musket ball passing through a little above the elbow an artery divided the arm was immediately amputated. Put on sick list, 25 July 1797. Discharged 20 August 1797 to HMS Seahorse.
ADM 101/120/6B Medical and surgical journal of HMS Seahorse for 20 August 1797 to 18 August 1799 by Thomas Eshelby, Surgeon, during which time the said ship was employed in the Channel, Bay of Cadiz, Mediterranean and blockade of Alexandria. Folio 1: Rear Admiral Sir Horatio Nelson; disease or hurt, amputation of right arm. Put on sick list, 20 August 1797 (continued from the Theseus's journal). Discharged 1 September 1797. The Surgeon was appointed from the Theseus to attend the Admiral to England. He landed at Portsmouth, 1st September [1797], would not suffer the ligature to be touched
ADM 101/124/1B Medical and surgical journal of HMS Vanguard for 17 June to 23 December 1798 by Michael Jefferson, Surgeon, during which time the said ship was employed in the Mediterranean. Folio 14: Sir Horatio Nelson, KCB, Rear Admiral of the Blue, aged 40; disease or hurt, wound on the forehead, over the right eye, the cranium bare for more than an inch, the wound three inches long. Put on sick list, 1 August 1798 off the Nile. Discharged 1 September 1798. The wound was perfectly healed on the first September, but as the integuments were much enlarged, I applied (every night) a compress wet with a discutient embrocation for nearly a month which was of great service.
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