Fix (remaining?) scoping issues #104
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added 5 commits
February 26, 2015 13:42
Fixes most things in scoping of constraints and conditions, but breaks conditional dbRDA (capscale).
capscale updated formula with a new data calculated within the function, and the environmental of the formula vanished after exiting. This could cause problems when the result was reused in anova.cca etc, or when capscale was embedded in other functions. tests/vegan-tests.R failed in all capscale cases before this fix.
All #FIXME# cases work now. These were about capscale, but work after 41847c6. Tests with anova.ccabyterm and anova.ccabymargin still fail because these functions refuse to handle missing values.
This was referenced Feb 27, 2015
jarioksa
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Feb 28, 2015
Fix (remaining?) scoping issues
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After this PR,
tests/vegan-tests.Rdo not fail in scoping issues. Two things were fixed:ordiParseFormulaevaluates models slightly differently when the terms are given indata=(which used to work) and when they are inatttached data frame or in global environment (which often failed). This also seems to fix cases where the terms in global environment had the same names as functions.capscalecalculated new data andupdated formula within the function when callingordiParseFormula, and the environment of the updated formula vanished after exiting or could not be scoped properly in embeddedcapscale. Now formula is evaluated in more standard ways.The
anova.ccabymarginandanova.ccabytermstill fail intests/vegan-tests.Rbecause we have not yet implemented handling of missing values in these functions.This seems to fix issues #16 and #100