Inconsistent atomic function inputs

Some functions like DiffCorr() and ResidualCorr() have similar function arguments, but their atomic functions don't share the same default argument values. It causes confusion when using them side by side.

.DiffCorr <- function(exp, obs, ref, N.eff = NA, method = 'pearson', alpha = NULL, handle.na = 'return.na') {
.ResidualCorr <- function(exp, obs, ref, N.eff, method, alpha, handle.na) {

Besides, some atomic function arguments have default values just like the main functions but some don't. Check all the functions and give the default values if possible.