Error in cor(as.vector(xdis), ydis, method = method, use = use) : missing observations in cov/cor about linket HOT 4 CLOSED

Hi Houyun,

Update

I noticed that when the table has the number value as "0", the error warning appeared.

Table screenshot

Error screenshot

Best,

Bing

from linket.

If I have a matrix with the first whole column of 0 in the matrix. Should I directly delete it from the data frame?

Data frame screenshot

Best,

Bing

from linket.

Hi Bing

I think this happens because the default distance method of spec is bray, but for the bray distance method, the row sum of the data (for each selected group) cannot be 0. So, you can solve this problem by setting the parameter spec_dist = dist_func(.FUN = "vegdist", method = "euclidean").

library(linkET)
set.seed(123)
spec <- data.frame(x = sample(0:2, 100, TRUE), y = sample(0:2, 100, TRUE))
env <- data.frame(x = rnorm(100), y = rnorm(100))

## Error: Reproduce your question
mantel_test(spec, env)
## OK
mantel_test(spec, env, spec_dist = dist_func(.FUN = "vegdist", method = "euclidean"))

from linket.

Hi Bing

I think this happens because the default distance method of spec is bray, but for the bray distance method, the row sum of the data (for each selected group) cannot be 0. So, you can solve this problem by setting the parameter spec_dist = dist_func(.FUN = "vegdist", method = "euclidean").

library(linkET)
set.seed(123)
spec <- data.frame(x = sample(0:2, 100, TRUE), y = sample(0:2, 100, TRUE))
env <- data.frame(x = rnorm(100), y = rnorm(100))

## Error: Reproduce your question
mantel_test(spec, env)
## OK
mantel_test(spec, env, spec_dist = dist_func(.FUN = "vegdist", method = "euclidean"))

In the next update, I'll be more careful with spec's default distance algorithm.

from linket.