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The compare() function reuses the variable wh for two unrelated purposes and doesn't seem to fit the use for contrasts construction variable cc at the end for some cases:
wh is first defined as:
wh <- is.na(pv$predicted.value)And then, inside the PVAL branch it is redefined, and only when if length(nterm) > 1:
wh <- coefs[, 1] == 0however the term is then used again outside if length(nterm) > 1:
cc <- list(coef = (1:lenf)[!wh], type = "con", comp = mat)which would still point to the first definition is.na(pv$predicted.value) in some branch of the evaluation?
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questionFurther information is requestedFurther information is requested