CODEWITHSUNDEEP
rvegan
Mauro Marcinkevicius
Mauro Marcinkevicius

Reputation: 11

Error in betadisper function - vegan package

I am trying to run the betadisper function (vegan package) and it returns an error. This is what I do:

hom.cov <- betadisper(morf.dist, sexo)

and it retorns to me this error: 

Error in sort.list(y) : 'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?

Then I run to traceback:

traceback()
5: stop("'x' must be atomic for 'sort.list'\nHave you called 'sort' on   
a list?")
4: sort.list(y)
3: factor(x)
2: as.factor(group)
1: betadisper(morf.dist, sexo)

When I saw this I tried to convert the vector "sexo" in factor with "as.factor" and then run again, but it returned to me the same error. So I tried to run "betadisper()" with the example use in "Numerical Ecology with R" and give me another error:

env <- read.csv("DoubsEnv.csv", row.names=1)
env.pars2 <- as.matrix(env[, c(1, 9, 10)])
env.pars2.d1 <- dist(env.pars2)
(env.MHV <- betadisper(env.pars2.d1, gr))
Error in x - c : arreglos de dimensón no compatibles

traceback()
2: Resids(vectors[, pos, drop = FALSE], centroids[group, pos, drop =   
FALSE])
1: betadisper(env.pars2.d1, gr)

I don't know what could happend. Can anyone help me?

Thanks!

Upvotes: 1

Views: 177

Answers (1)

Jari Oksanen
Jari Oksanen

Reputation: 3682

R claims that sexo is not atomic. This is not the most obvious message, but it means that sexo is not a simple vector of values, but it may be, say, a data frame or a list. Issue

str(sexo)

and see what you get. If you see text like data.frame or list in the output and then a dollar sign ($) then you don't have a simple structure. For instance, the following output is not an atomic item:

> str(a)
List of 1
  $ a: Factor w/ 4 levels "BF","HF","NM",..: 4 1 NA 4 2 2 2 2 2 1 ...

In this case you should use a$a instead of only a.

Upvotes: 1

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