Extract R2 values from multiple adonis results - r

Question

I am wondering if there is some way how to extract results from adonis function in vegan package and possibly save it by write.table?
I mean other way than print results to console and copy-past R2 value to Excel.
This can be especially useful when running adonis iteratively for multiple combinations and saving objects with results into one list as suggested in this SO answer.

Answer 1

Here is an example on how you can extract the needed parameters from the model. I will use the linked example:
library(vegan)
data(dune)
data(dune.env)
lapply is used here instead of a loop:
results <- lapply(colnames(dune.env), function(x){
form <- as.formula(paste("dune", x, sep="~"))
z <- adonis(form, data = dune.env, permutations=99)
return(as.data.frame(z$aov.tab)) #convert anova table to a data frame
}
)
this will produce a list of data frames each having the form
> results[[1]]
#output
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
A1 1 0.7229518 0.7229518 3.638948 0.1681666 0.01
Residuals 18 3.5760701 0.1986706 NA 0.8318334 NA
Total 19 4.2990219 NA NA 1.0000000 NA
now you can name the list elements with the appropriate variable:
names(results) <- colnames(dune.env)
convert to a data frame:
results <- do.call(rbind, results)
#output
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
A1.A1 1 0.7229518 0.7229518 3.638948 0.1681666 0.01
A1.Residuals 18 3.5760701 0.1986706 NA 0.8318334 NA
A1.Total 19 4.2990219 NA NA 1.0000000 NA
Moisture.Moisture 3 1.7281651 0.5760550 3.585140 0.4019903 0.01
Moisture.Residuals 16 2.5708567 0.1606785 NA 0.5980097 NA
Moisture.Total 19 4.2990219 NA NA 1.0000000 NA
Management.Management 3 1.4685918 0.4895306 2.767243 0.3416107 0.01
Management.Residuals 16 2.8304301 0.1769019 NA 0.6583893 NA
Management.Total 19 4.2990219 NA NA 1.0000000 NA
Use.Use 2 0.5531507 0.2765754 1.255190 0.1286690 0.30
Use.Residuals 17 3.7458712 0.2203454 NA 0.8713310 NA
Use.Total 19 4.2990219 NA NA 1.0000000 NA
Manure.Manure 4 1.5238805 0.3809701 2.059193 0.3544714 0.03
Manure.Residuals 15 2.7751414 0.1850094 NA 0.6455286 NA
Manure.Total 19 4.2990219 NA NA 1.0000000 NA
and now you can save it to a csv or any other format you like:
write.csv(results, "res.csv")
If only R squared is needed change the lapply call to:
results <- lapply(colnames(dune.env), function(x){
form <- as.formula(paste("dune", x, sep="~"))
z <- adonis(form, data = dune.env, permutations=99)
return(data.frame(name = rownames(z$aov.tab), R2 = z$aov.tab$R2))
}
)