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rplotaxis-labelsvegan

No axes labels showing in NODF plot of R

I am having problems revealing axis values in R. I am running a test on nestedness using the vegan package. The function is working, but my problem comes from the plotting. The ordering of the values are not explained. I chose to use the nestednof(x, order = TRUE) command to see what nestednodf would came up with. Using the nodf order, R found my sites to be nested, but I do not know which columns are which sites and which row are which species. 

nn  <- nestednodf(PA4N)
plot(nn)

Order = TRUE

After not being able to figure out what my graph is showing I chose to use order = TRUE. I know which site is which and which species are which, except it is not as nested as the nestednodf(x, order = TRUE).

nnf <- nestednodf(PA4N, order = FALSE)
plot(nnf)

Order = FALSE

Any advice on how R can show the names of the rows and columns?

Lastly, my rows are sites going west to east as columns. The presence and absence of snails following the sites they are in as rows.

Solution

  • You need to set the names flag to TRUE. See ?nestednodf for details.

    library(vegan)
data(sipoo)
plot(nestednodf(sipoo), names= TRUE)