- An argument for significance level alpha is given in the example code (readme) which is not used for the computation (default is 0.05).
- The function testThenRank has an argument FUN that is set to "significance" internally. The value that is actually passed is not used. Should "significance" be the default value in the signature already or should the argument be removed?
- The parameters should be given in the report for reproducibility.
This was a tricky bug, thanks!
alpha is now respected, argument FUN is removed. significance ranking is considered an aggregation step, so testThenRank() is nothing else than aggregateThenRank(FUN="significance").
Note that testThenRank will pass all arguments to decision.challenge(), i.e. it will respect arguments:
na.treat=NULL, alpha=0.05, p.adjust.method="none", alternative="one.sided", test.fun=function(x,y) wilcox.test(x,y, alternative = alternative,exact=FALSE, paired = TRUE)$p.value, parallel=FALSE, progress="none"