Adonis Table

adonis_table.R

adonis_table <- function(phy, d, ...){
	subs <- function(dist, index) as.dist(as.matrix(dist)[index,index])
	contcheck <- function(var){
		suppressWarnings(
		if(all(is.na(as.numeric(var))) | length(unique(var))<10){
			return(var)
		} else {
			return(as.numeric(var))
		}
		)
	}
	tab <- phy %>%
		get_variable(.) %>%
		gather(variable, value, ...) 
	tab %>% 
		group_by(variable) %>%
		do( adonis(subs(d,!is.na(.$value)) ~ contcheck(value), .[!is.na(.$value),]) %>% 
			( function(x) {data.frame(	x$aov.tab[1,4:6], 
										n = nrow(x$model.matrix),
										perms = nrow(x$f.perms)
										)} )
			) 	 %>%
		ungroup %>%
		rename(pval = `Pr..F.`)
}