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JoshuaZ comments on Funnel plots: the study that didn't bark, or, visualizing regression to the null - Less Wrong
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They are useful for showing publication bias when the bias is not in a subtle form. But they aren't great for subtle biases. Also, a distorted funnel plot can be caused by other issues. Some types of measurement errors and statistical biases can result in weird results on a funnel plot. Like any specific tool, they have definite limits and should be used in conjunction with other tools.