My data is percentage disease data of different varieties of plants that had been inoculated with disease from several different sources. having conducted two-way ANOVA in SPSS (using the log10+1 of my proportions (+1 due to some zero percents in the data)) I find that my data fails homogeneity of variance but (mostly) normally distributed. I have analysed residuals and found that this appears to caused by one of the inoculated varieties which has data skewed towards zero percent seemingly irrespective of disease source.
Our resident statistician has looked at my data and told me that perhaps my best option is to use a beta distributed GLM, as I need to be able to reliably determine if there is an interaction between the two independent variables. However despite learning as much as I can about this over the last couple of days, I am unsure how best to implement this in R, and have no idea how to determine whether or not this is a valid fit for my data (this is where I am most stuck).