Atterbury's treatise, though highly praised by Bishop Gilbert Burnet, was more distinguished for the vigour of his rhetoric than the soundness of his arguments, and the Papists accused him of treason, and of having, by implication, called King James "Judas".
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He was figured by Swift in the Battle of the Books as the Apollo who directed the fight, and was, no doubt, largely the author of Boyle's essay.
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He inspired a pupil, Charles Boyle, in the Examination of Dr. Bentley's Dissertations on the Epistles of Phalaris, an attack (1698) on the Whig scholar Richard Bentley, arising out of Bentley's impugnment of the genuineness of the Epistles of Phalaris.
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In the ninth year of his banishment he published a vindication of himself against John Oldmixon, who had accused him of having, in concert with other Christ Church men, garbled the new edition of Clarendon's History of the Rebellion.
He briefly returned to Ireland again, visiting his parents, and returned to London, taking up employment under a Roman Catholic named Clifton, meeting Atterbury, Bishop of Rochester, for whom he printed a defence of an imprisoned Clergyman.
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