Changing confidence level
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It is not very clear from the vignette, what you can actually specify in the test.args argument. However, I would like to change the confidence level of the test. Is that possible?
The test.args argument is passed to the wilcox.test or t.test function call, so you would have to look in their documentation. You can use the test.args argument for example to specify if a paired test is done or if you want to do a one sided test (i.e. test.args=list(paired=TRUE, alternative="less")).
To change the signficance levels you have to change the map_signif_level argument like this map_signif_level =c("***"=0.0005, **"=0.005, "*"=0.05) argument.
I hope this answers your question and I will thus close the issue for now. If I misunderstood your question, feel free to just comment below.