tidy_rarecurve.R

#' Convert vegan rarecurve results to tidy format
#'
#' @param x a list of rarefy results returned by rarecurve
#' @param sites a vector of site names
#'
#' @return A data.frame in "long format".
#'
tidy_rarecurve <- function(x, sites) {
  long_list <- mapply(function(x, sites) {
    data.frame(
      site = sites,
      samp_names = names(x),
      samp_size = attr(x, "Subsample"),
      species = x)},
    x = x, sites = sites, SIMPLIFY = FALSE)
  
  do.call(rbind, long_list)
}


# DEMO

library(vegan)
library(ggplot2)
library(magrittr)

data(BCI)

# Fit rarefaction curves with vegan
rc <- rarecurve(BCI, step = 20, col = "blue", cex = 0.6)

# Tidying
tidy_rc <- tidy_rarecurve(rc, sites = rownames(BCI))

# Plot with ggplot
tidy_rc %>% 
  ggplot() +
  geom_line(aes(samp_size, species, group = site))