To simplify, I have a data set which is as follows:
b <- 1:6
# > b
# [1] 1 2 3 4 5 6
jnk <- c(2, 4, 5, NA, 7, 9)
# > jnk
# [1] 2 4 5 NA 7 9
When I try:
cor(b, jnk, na.rm=TRUE)
I get:
> cor(b, jnk, na.rm=T)
Error in cor(b, jnk, na.rm = T) : unused argument (na.rm = T)
I've also tried na.action = na.exclude, etc. None seem to work. It'd be really helpful to know what the issue is and how I can fix it. Thanks.
Answer
TL; DR: Use instead:
cor(b, jnk, use="complete.obs")
Read ?cor:
cor(x, y = NULL, use = "everything",
method = c("pearson", "kendall", "spearman"))
It doesn't have na.rm, it has use.
an optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings
"everything","all.obs","complete.obs","na.or.complete", or"pairwise.complete.obs".
Pick one. Details of what each does is in the Details section of ?cor.