How would I go about making rank abundance curves to compare tree species from two different years? I dont have data to share here, but any general code guidance would be very helpful!
Hi, perhaps try
@williaml thanks. I did see that in my search, but I am having a hard time interpreting what they are describing to make code out of it. Or rather I am not sure where to plug things in to compare the abundance of 15 species (the species are in one column) in two different years...
This is the example dataset that they use: R: Vegetation releves from Scheden (r-project.org)
Your species are in one column, but you could use something like
dplyr::pivot_wider() to get them in to many columns so that they're in the same shape.
See also: R: Rank Abundance Curves (r-project.org)
I was curious what a rank abundance curve is.
It may be of advantage to feed it in into a dedicated package, maybe you want to obtain some other parameters describing or differentiating the curves / populations (see: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.2881)
However the plot is quite simple, you just need the rank and the abundance (the counts?)
library(tidyverse) # Calculate values based on the diamonds dataset rank_abundance = diamonds %>% # count count(cut, color, name = "abundance") %>% # add ranks within the readout groups (here: cut) group_by(cut) %>% mutate(rank = rank(desc(abundance))) %>% # add normalised abundance mutate(norm_abundance = abundance / max(abundance)) # check the outcome rank_abundance # A tibble: 35 x 5 # Groups: cut  cut color abundance rank norm_abundance <ord> <ord> <int> <dbl> <dbl> 1 Fair D 163 6 0.519 2 Fair E 224 4 0.713 3 Fair F 312 2 0.994 4 Fair G 314 1 1 5 Fair H 303 3 0.965 6 Fair I 175 5 0.557 7 Fair J 119 7 0.379 8 Good D 662 5 0.710 9 Good E 933 1 1 10 Good F 909 2 0.974 # ... with 25 more rows # plot with total abundance ggplot(rank_abundance, aes(x = rank, y = abundance)) + geom_line() + geom_point(aes(colour = color), size = 4) + theme_bw() + facet_wrap(~ cut)
# plot with normalised abundance ggplot(rank_abundance, aes(x = rank, y = norm_abundance)) + geom_line() + geom_point(aes(colour = color), size = 4) + theme_bw() + facet_wrap(~ cut) # all in one ggplot(rank_abundance, aes(x = rank, y = abundance, colour = cut)) + geom_line() + geom_point(size = 7) + geom_text(aes(label = color), colour = "grey70", fontface = "bold") + theme_bw()
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