This directory contains a PDF version of: Stone, G. N., S. Nee, and J. Felsenstein. 2011. Controlling for non-independence in comparative analysis of patterns across populations within species. Philosophical Transactions of the Royal Society B 366 (1569): 1410-1424. as file StoneNeeFelsenstein2011.pdfPlease note carefully that these papers, as published in the journals, are copyright to the publishers of those journals.
Note that the equations describing my methods in this paper are mostly wrong. I complained about this, but the other authors said this would be "clearer to the readers", and I was outvoted. For more correct equations see my 2002 paper.