Scoping issues in anova.ccaby* methods #101
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February 23, 2015 13:28
This fails: data(dune, dune.env) cca <- dune m <- cca(cca ~ ., dune.env) anova(m, by="term") ... and ordiParseFormula finds function cca() instead of data "cca"
Benedicte Bachelot reported that anova.cca(..., by=) cases fail if community data had the same name as some function. She called her community data 'all' (which is a primitive), but any other function name was found before data. Changes in scope fix the reported case, but there are still other cases where the same confusion occurs. The initial report was emailed to me on 21/2/2015.
Fixes some (but not all) scoping issues
There are still a couple of cases that fail, but these are now more clearly marked as FIXME
Embed rda in a function used in lapply(). This tests failed yesterday, but it worked when I got it: some fix in scoping issue automatically fixed this, too.
envdepth argument was kluge released in vegan 1.15-0 (Sep 30, 2008) to handle some problems with capscale. This never really worked, and the ChangeLog of the kluge put it: "(The environment() drives me crazy, says J.O.)"
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@jarioksa This looks good and the fix (evaluating in the environment of the formula) is mentioned as a fix to the "bug" in I'm going to merge this... |
gavinsimpson
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Feb 25, 2015
Scoping issues in anova.ccaby* methods
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There were too almost simultaneous reports on scoping issues. Benedicte Bachelot reported that
anova.ccabytermfailed when the community data had a name of a function. She hadall, and the test case hasA couple of days later, Richard Telford tweeted about problems in embedding
anova.ccabymargininlapply, and @gavinsimpson raised this as issue #100. When testing this, I noticed that the fix made for the Bachelot case also corrected this issue.I am not quite sure that this PR is completely safe: environments are a pain. However, all old test cases pass and some that failed earlier also work now. Some scoping issues still remain, but the reported bad cases were corrected. Better make this public for review, though.