I would like to see if the distribution of my species is affected by specific environmental parameters. When I try to do the analysis with the function "capscale ()" the graph showed only the first 5 variables of the 20 total. Please, can someone help me? Thanks. This is the code I used.
species <- read.table('db-RDA.txt', sep ='\t', h = T, strip.white = T)
species = species[,2:ncol(species)]
species001= (species + 0.001)
fix(species001)
env <- read.table('Env Db-RDA.txt', sep ='\t', h = T, strip.white = T)
env = env[,-1]
env001= (env + 0.001)
fix(env001)
#I have not put all variables but only appeared the first 5 explanatory variables
dbRDA = capscale(species001 ~ Rock + Sand + Rubble + pH + NOx + NH4 + Temp + SIOH + DIC, data=env001, dist = "bray", scale=TRUE)
plot(dbRDA)
I guess that the function told you that some of your variables were aliased. Aliasing means that these variables are linear combinations of some other variables in the model, and there is no independent information to estimate those. See what the output says when you just call the short description of your result. You can get this by typing the name of the result as
dbRDA.