Hi everyone, Since I've noticed this problem has been seen before, I figured I would update the list with my potential solution. The problem was that the pgls breaks multi-state categorical variables into a number of binary variables (like shown by the summary function). This increases the number of variables that the anova then tries to iterate over, but there are fewer variables in the formula, so it hits an error where it doesn't know what other variables to include. I fixed this by having it iterate over the number of variables in the formula rather than the number of binary variables. I've attached the fixed anova.pgls script here. It's been working for me and two other users confirm that it is working for them as well. If you do use the script and it solves your problems, please let me know. -Will
On Sat, Mar 7, 2015 at 10:20 PM, William Gearty <wgea...@stanford.edu> wrote: > Hi all, > I've noticed that a number of people have had this problem, but can't seem > to find any resolutions. > I am running a PGLS analysis, with body size as the dependent variable, > and two categorical traits as the explanatory variables: > >> data.pgls <- pgls(MeanBodyMass ~ Habitat_aq * TrophicLevel, species.comp, >> lambda='ML', delta='ML') >> > The pgls runs without any problems, and summary(data.pgls) gives proper > results. > However, when I run anova(data.pgls), I get the following error: > >> Error in terms.formula(formula, data = data) : >> invalid model formula in ExtractVars > > My trophic level categorical explanatory variable is multistate (not > binary), so the anova results are much preferred to the summary results > (which splits multistate variables into a number of binary ones). > Has anyone run into this problem before and has found a fix or workaround? > Thanks once again in advance, > Will > > -- > William Gearty > PhD Student, Paleobiology > Department of Geological and Environmental Sciences > Stanford School of Earth, Energy & Environmental Sciences > people.stanford.edu/wgearty > -- William Gearty PhD Student, Paleobiology Department of Geological and Environmental Sciences Stanford School of Earth, Energy & Environmental Sciences people.stanford.edu/wgearty
anova.pgls.fixed.r
Description: Binary data
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