Why does my plot have these sit labels all over it? I am plotting an RDA

Question

library(vegan)
buoy.rda <- rda(buoy_means, weather)
ef <- envfit(buoy.rda, weather, permutations = 1000)
ef
plot(buoy.rda)
plot(ef)

The buoy_means file columns are labeled by buoy ID (which is the red blob) not sit#

Answer 1

The red labels are the column names of your first matrix (X, or buoy_means in your case), the blue labels (and arrows) correspond to the column names of the second matrix (Y, or weather in your case), and the black labels are the row names of both X and Y (since they should match).

By default, sites, species and "biplot arrows" are displayed byt the plot function. To know more about that, see the help file of plot.cca (?plot.cca). The argument to change to have a different behaviour is display:

display Scores shown. These must include some of the alternatives "species" or "sp" for species scores, sites or "wa" for site scores, "lc" for linear constraints or LC scores, or "bp" for biplot arrows or "cn" for centroids of factor constraints instead of an arrow, and "reg" for regression coefficients (a.k.a. canonical coefficients). The alternative "all" selects all available scores.

Example with sites on plot

data(dune)
data(dune.env)
dune.Manure <- rda(dune ~ Manure, dune.env)
plot(dune.Manure) 

and without sites

plot(dune.Manure, display = c("sp", "bp"))