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Heat the oven to 200C/180C fan/gas 6. Toss the beetroot and onion with the oil, honey and vinegar, then season. Tip into a 20cm non-stick ovenproof frying pan. Cover with foil and roast in the oven for 45-50 mins until the beetroot is tender. Remove from the oven and scatter over the butter and thyme.
Roll the pastry out on a lightly floured surface to the thickness of a £1 coin, then cut out a circle slightly larger than the frying pan, about 25cm (you can use a dinner plate as a guide). Lay the pastry over the beetroot mixture in the pan, and tuck it in around the edge using a cutlery knife or spatula. Bake for 50-60 mins, or until golden brown and puffed up.
Run a knife around the edge of the pastry to loosen, then carefully invert onto a serving plate. Scatter over the pecans and cheese to finish.