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 1642 he was in repeated correspondence with G. J. Vossius. As early as June 1631 Farnaby had bought a country house at Sevenoaks, and the plague of 1636 (combined with a quarrel with his London landlord) induced him to remove his school there. The school throve, and Farnaby bought much land at Sevenoaks as well as estates at Otford, Kent, and Horsham, Sussex. His reputation as a classical scholar led to a commission from the king to prepare a new Latin grammar to replace the one already in use in the public schools. On 10 July 1641 Farnaby petitioned the House of Lords to secure his grammar, then just completed, the monopoly promised it by Charles I (Hist. MSS. Comm. 4th Rep. 866). The civil wars ruined Farnaby. He was reported to have said that he preferred one king to five hundred. In 1643 he was arrested by the parliamentarians near Tunbridge, and was committed to Newgate. He was placed on board ship with a view to his transportation to America, but was ultimately sent to Ely House, Holborn, where he was detained for a year. He was allowed to return to Sevenoaks in 1645, and he died there 12 June 1647, being buried in the chancel of the church.

Farnaby married, first, Susan, daughter of John Pierce of Lancells, Cornwall; and secondly, Anne, daughter of John Howson, bishop of Oxford, afterwards of Durham. By his first wife he had (besides a daughter Judith, wife to William Bladwell, a London merchant) a son, John, captain in the king's army, who inherited his father's Horsham property, and died there early in 1673. By his second wife he had, among other children, a son Francis, born about 1630, who inherited the Kippington estate, Sevenoaks, and was a widower on 26 Jan. 1662–3, when he obtained a license to marry Mrs. Judith Nicholl of St. James, Clerkenwell (, Marriage Licenses, ed. Foster, p. 471).

Farnaby was the chief classical scholar as well as the chief schoolmaster of his time. His editions of the classics, with elaborate Latin notes, were extraordinarily popular throughout the seventeenth century. He edited Juvenal's and Persius's satires (Lond. 1612, dedicated to Henry, prince of Wales, 1620, 1633, 1685 tenth ed.); Seneca's tragedies (Lond. 1613, 1624, 1678 ninth ed., 1713, 1728); Martial's ‘Epigrams’ (Lond. 1615, Geneva, 1623, Lond. 1624, 1633, 1670, seventh ed.); Lucan's ‘Pharsalia’ (Lond. 1618, 1624, 1659, seventh ed.); Virgil's works (1634, dedicated to Lord Craven of Hamsted, and 1661); Ovid's ‘Metamorphoses’ (Lond. 1637, 1650, 1677, 1739); Terence's comedies, ed. Farnaby and Meric Casaubon (Amsterdam, 1651, 1669, 1686, 1728, Saumur, 1671).

Farnaby's other works are: 1. ‘Index Rhetoricus Scholis et Institutioni tenerioris ætatis accommodatus,’ London, 1625; 2nd ed. 1633; 3rd ed. 1640; 4th ed. 1646; 15th ed. 1767; reissued in 1640 as ‘Index Rhetoricus et Oratoricus cum Formulis Oratoriis et Indice Poetico,’ and epitomised by T. Stephens in 1660 for Bury St. Edmunds school under the title ‘Tροποσκηματολογία.’ 2. ‘Phrases Oratoriæ elegantiores et poeticæ,’ London, 1628, 8th ed. 3. ‘Ἡ τῆς Ἀνθολογίας Ἀνθολογία, Florilegium Epigrammatum Græcorum eorumque Latino versu a variis redditorum,’ London, 1629, 1650, 1671. 4. ‘Systema Grammaticum,’ London, 1641; the authorised Latin grammar prepared by royal order. 5. ‘Phrasiologia Anglo-Latina,’ London, 8vo, n.d. 6. ‘Tabulæ Græcæ Linguæ,’ London, 4to, n.d. 7. ‘Syntaxis,’ London, 8vo, n.d. A patent dated 6 April 1632 granted Farnaby exclusive rights in all his books for twenty-one years (, Fœdera, xix. 367), and on the back of the title-page of the 1633 edition of the ‘Index Rhetoricus’ penalties are threatened against any infringement of Farnaby's copyright. In both documents mention is made of editions by Farnaby of Petronius Arbiter's ‘Satyricon’ and Aristotle's ‘Ethics,’ but neither is now known. Letters from Vossius to Farnaby appear in Vossius's ‘Epistolæ’ (Lond. 1690), i. 193, 353, 386. Four of Farnaby's letters to Vossius are printed in Vossius's ‘Epistolæ Clarorum Virorum’ (1690), pp. 70, 85, 213, 303. Other letters appear in John Borough's ‘Impetus Juveniles’ (1643), and in Holyday's ‘Juvenal.’ Farnaby prefixed verses in Greek with an English translation to Coryat's ‘Crudities,’ and he wrote commendatory lines for Camden's ‘Annales.’

Ben Jonson was a friend of Farnaby, and contributed commendatory Latin elegiacs to his edition of Juvenal and Persius. John Owen praises Farnaby's Seneca in his ‘Epigrams.’ He is highly commended in Dunbar's ‘Epigrammata,’ 1616, and in Richard Bruch's ‘Epigrammatum Hecatontades duæ,’ 1627.

[Wood's Athenæ Oxon., ed. Bliss (partly communicated by Farnaby's son Francis), iii. 213–16; Visitation of London, 1633–5 (Harl. Soc.), i. 265; Wood's Fasti, i. 367; Lady Fanshawe's Memoirs, p. 59; P. Cunæi Epistolæ, Leyden, 1725, p. 318; Vossii Epistolæ, Lond. 1690; Professor Mayor also refers in Notes and Queries, 2nd ser. xi. 338, to Wheare's Characteristica, p. 130, and to the same writer's Epistolæ Euclidisticæ, No. 50, p. 77. Early manuscript notes are to be found in one of the 1629 editions of Farnaby's Florilegium at the Bodleian Library, and in the 1633 edition of the Index Rhetoricus at the British Museum.] 