data-raw/Assays/assays.R

In mwhalen18/krspfecals: KRSP Auxilary Fecal Database

#loading eia data
library(stringr)
library(readr)
library(janitor)

assays = read_csv("data-raw/Assays/fecal_database.csv") %>% clean_names() %>%
  rename(poop_id = poop_vial_id) %>%
  mutate(poop_id = str_extract_all(poop_id, "([A-Z]{1}[0-9]{3,4}|[0-9]{1,3}-[0-9]{2})|[0-9]{5}")) %>%
  select(-c(extra_fecal_sample, duplicate_sample, field_poop_vial_id, poop_time)) %>%
  rename(sample_assayed_if_two_samples = sample_extracted_if_two_samples)


assays$third_poop_id = sapply(assays$poop_id, function(x){
  nth(x, 3)
})
assays$second_poop_id = sapply(assays$poop_id, function(x){
  nth(x, 2)
})
assays$poop_id = sapply(assays$poop_id, function(x){
  nth(x, 1)
})

#Fix known issues
assays = assays %>%
  mutate(sample_assayed_if_two_samples = case_when(
    poop_id == "P1620" ~ "P1669",
    TRUE ~ as.character(sample_assayed_if_two_samples)
  ))


usethis::use_data(assays, overwrite = TRUE)