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. 2019 Apr 4;19(3):623–638. doi: 10.1111/1755-0998.12994

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© 2019 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Natural setups: quality assessment is performed for LDhat and LDJump based on the proportion of correctly identified hotspots (PCH, top‐left), the proportion of correctly identified background rates (PCB, top‐right), the average performance (AP = (PCH+PCB)/2, bottom‐left), the estimated number of blocks (bottom‐middle), and the weighted RMSE (bottom‐right). Based on 13 setups with 20 replicates these measures are computed for LDJump using different numbers of initial segments k (500, 1,000, 1,500, 2,000) and compared with the results from rhomap of LDhat using a block penalty of 50 [Colour figure can be viewed at wileyonlinelibrary.com]