PEER (Publishing and the Ecology of European Research), supported by the EC eContentplus programme, has been investigating the potential effects of the large-scale, systematic depositing of authors' final peer-reviewed manuscripts (so called Green Open Access or stage-two research output) on reader access, author visibility, and journal viability, as well as on the broader ecology of European research. The project ran from 1 September 2008 - 31 May 2012. This is PEER final report.