Q:

correlation of two ordinal variables in R

I want to test the spearman correlation of two ordinal variables.
x=c(1,2,3)
y=c(4,3,6)
x=ordered(x)
y=ordered(y)
cor(x,y,methods="spearman")

I always get "Error in cor(x, y) : 'x' must be numeric"
what's the correct way to do this?

A:

Two methods:

use as.numeric. 
x=c(1,2,3)
y=c(4,3,6)
x=ordered(x)
y=ordered(y)
cor(as.numeric(x), as.numeric(y), method="spearman")
[1] 0.5

Note that this is not treating x and y simply as continuous numbers. It is treating them as ranks. 
as.numeric(y)
[1] 2 1 3

This method will allow you to ignore NA values.
x=c(1,2,3, NA)
y=c(4,3,6, 7)
x=ordered(x)
y=ordered(y)
cor(as.numeric(x), as.numeric(y), 
    method="spearman", use="pairwise.complete.obs")
[1] 0.5

You can use the package pspearman which will handle the ordered factor. 
x=c(1,2,3)
y=c(4,3,6)
x=ordered(x)
y=ordered(y)

library(pspearman)
spearman.test(x,y)

Spearman's rank correlation rho

data:  x and y
S = 2, p-value = 1
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho 
0.5 

Or if you want to reduce some of the output,  you could use:
spearman.test(x,y)$estimate
rho 
0.5 

