Hello. I'm not sure which variable refers to Region in your sample data. But here's the general tidyverse way of generating frequency tables. For the example below I'm counting Status by Site and filtering for only positive cases.
library(dplyr, warn.conflicts = FALSE)
df <- tibble(Site = c("HPK", "HPK", "HPK", "UUK"),
Status = c("positive", "negative", "negative", "negative"))
df %>%
count(Site, Status) %>%
filter(Status == "positive")
#> # A tibble: 1 x 3
#> Site Status n
#> <chr> <chr> <int>
#> 1 HPK positive 1
Created on 2020-09-03 by the reprex package (v0.3.0)