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 to exercise a paramount influence in the parliament which assembled in 1690, but his attempted alliance with them gave deep offence to a large number of presbyterians, especially after the discovery of the Jacobite plot, and, as many waverers were also won over ‘by money and other gratifications,’ as well as by assurances of the king's good-will to the presbyterians (see Instructions from the King to Lord Melville in Leven and Melville Papers, pp. 417–18), and by the manifestation of a willingness to compromise some of the matters in dispute, the deadlock was soon at an end. Without any further mention of the acts aimed against the Dalrymples, an extraordinary supply to meet the expenses caused by the Jacobite insurrection was voted, amounting to 162,000l. On the proposal of Dalrymple a statute was passed establishing presbyterian church government mainly on the basis of the settlement of 1592, with the adoption of the Westminster Confession instead of that of Knox, in opposition to a motion of Sir James Montgomery for the express recognition of the covenant and all the standards of 1649. To further conciliate the presbyterians, an act was also passed for transferring the patronage of churches to the heritors and kirk sessions. In January 1691 Dalrymple, who, on the elevation of his father to the peerage in April 1690, had become Master of Stair, was appointed joint secretary of state along with Lord Melville, who, however, soon afterwards exchanged that office for the keepership of the privy seal, and was succeeded by Johnstone of Warriston.

Immediately after his appointment, Stair attended William on his visit to Holland. While there the king, under his direction, began to take more decisive measures for the settlement of the highlands, in regard to which negotiations had been for some time in progress with the Earl of Breadalbane [see first ]. In a letter of 17 Aug. to the privy council from the camp at St. Gerard, subscribed by Stair in the name of the king, the council were commissioned to issue a proclamation offering indemnity to all the clans who had been in arms, but requiring them to take the oath of allegiance in the presence of a civil judge before 1 Jan. 1692 (Letter and proclamation in Papers illustrative of the Highlands, pp. 33–7). From the letters of Stair it is evident that he would have much preferred that a considerable number of the clans should have stood out, in order that by a signal act of vengeance the highlanders might have been taught more effectually the danger of rebellion in the future. All that he had hoped or desired to result from the offer of indemnity and a gift of money for bribes to the Earl of Breadalbane, was that a certain proportion of the clans should have accepted the terms offered, thus rendering less difficult the execution of summary punishment upon the remainder. It was felt by the government that a submission, not in any degree inculcated by vengeance, could only be of a feigned and temporary character. Preparations had therefore been made for a winter campaign in the highlands, and before information had been received in London as to the result of the offer of indemnity, Sir Thomas Livingstone was ordered to ‘act against those highland rebels who have not taken the benefit of our indemnity, by fire and sword, and all manner of hostility.’ It so happened that MacIan, chief of the Macdonalds of Glencoe, was the only chief who had failed to comply with the letter of the proclamation, and even he had failed merely because he found no one at Fort William to tender him the oath when he presented himself there on 31 Dec. He induced the sheriff of Inverary to administer it on 6 Jan. after the period of grace had expired, but this availed him nothing. Stair, on learning from Argyll how matters stood with MacIan, expressed to Sir Thomas Livingstone his gratification, adding: ‘It is a great work of charity to be exact in rooting out that damnable sept, the worst in all the highlands.’ The additional instructions subscribed by the king on 16 Jan. contained also a proviso that ‘if MacIan and that tribe can be well separated from the rest it will be a proper vindication of the public justice to extirpate that sept of thieves.’ For all the details of the method by which the massacre of 13 Feb. was accomplished Stair cannot be held as immediately responsible, but there is undoubted evidence that the arrangements afterwards met with his full approval, his only regret being that they had not been more successful. It was some time before the particulars of the massacre came to be generally known, the earliest intimation of its occurrence being through letters in the ‘Paris Gazette’ in March and April of 1692, from information supplied by the Jacobites, probably with the view of awakening animosity against the government in the highlands.

Meantime the affairs of the church now for a year occupied the principal share of Stair's attention. An attempt was made to effect a union between the presbyterian and episcopal clergy, and finally, after the king had agreed to dispense with putting the oath of allegiance to every clerical member of the assembly about to meet, the assembly in 1693 appointed a commission to receive episcopal ministers