Plotting Rarefaction Curves in R (UPDATE)

In this video I demonstrate how to do rarefaction using the rarefy () function in the vegan package in R and plot rarefaction curves. Here's the code I ran in this video, but NOTE that Youtube does not allow angled brackets in video descriptions, so I could not type the assignment operator ("less than sign" plus "hyphen"): # Example code for generating and plotting a rarefaction curve # John Sakulich # 5 August 2024 # Read in a data set # These data are from Colorado Breading Bird Survey # for all individuals counted in the BBS in 1978 and 2018 birds -read.csv("Birds!.csv") # Calculate Species richness for each survey year (1978 and 2018) abundance.2018 - sum(birds$abundance_2018) abundance.1978 - sum(birds$abundance_1978) richness.2018 - sum(birds$abundance_2018 != 0) richness.1978 - sum(birds$abundance_1978 != 0) # Load in the vegan package library (vegan) rarefied.2018 - rarefy(birds$abundance_2018, 15905, se = TRUE) # Generate values for 2018 BBS data (221 total species) rare.2018 - rarefy(birds$abundance_2018,seq(1, 63594, by = 250) , se = TRUE) trare.2018 - t(rare.2018) rare.2018.df - as.data.frame(trare.2018) rare.2018.df$se.high - rare.2018.df$.S + rare.2018.df$.se rare.2018.df$se.low - rare.2018.df$.S - rare.2018.df$.se rare.2018.df$N - seq(1, 63594, by = 250) # Generate values for 1978 BBS data (143 total species) rare.1978 - rarefy(birds$abundance_1978,seq (1, 15905, by = 64) , se = TRUE) trare.1978 - t(rare.1978) rare.1978.df - as.data.frame(trare.1978) rare.1978.df$se.high - rare.1978.df$.S + rare.1978.df$.se rare.1978.df$se.low - rare.1978.df$.S - rare.1978.df$.se rare.1978.df$N - seq (1, 15905, by = 64) # Plot the 2018 BBS rarefaction curve with standard errors plot (rare.2018.df$N, rare.2018.df$.S, type = "l", xlim = c(1, 10000), lwd = 2, col = "firebrick4", cex = 2, xlab = "abundance level", ylab = "species richness", main = "Colorado Breeding Bird Survey 1978 and 2018") lines (rare.2018.df$N, rare.2018.df$se.high, type = "l", lty = "dashed", col = "firebrick4") lines (rare.2018.df$N, rare.2018.df$se.low, type = "l", lty = "dashed", col = "firebrick4") # Add the 1978 BBS data to the plot lines (rare.1978.df$N, rare.1978.df$.S, type = "l", lwd = 2, lty = "solid", cex = 2, col = "dodgerblue") lines (rare.1978.df$N, rare.1978.df$se.high, type = "l", lty = "dashed", col = "dodgerblue") lines (rare.1978.df$N, rare.1978.df$se.low, type = "l", lty = "dashed", col = "dodgerblue") legend (40000, 75, legend = c("BBS 2018", "BBS 1978"), col = c("firebrick4","dodgerblue"), lty=1:1, lwd = 2)