paired
By default, independence of the two groups or data sets is assumed. If the number of cases in x and y are equal and paired (e.g. pre-post) comparisons, this should be set to TRUE.
t.welch
By default, the variances of the two datasets are not assumed equal. If the pooled variance is needed for t, p, and df this should be set to FALSE. This setting has no effect on the calculation of Cohens'd.