ALL - missing sample check

[stephpenn1]

Example missing sample check from TCTN, fill in with analyte-specific column names:

# 5. Check with Metadata for missing:

source("./Processing_Scripts/Metadata_kit_list.R")

metadata_collected %>%
  filter(sample_method == "jar", transect_location != "sediment") -> meta_filter

data_clean %>%
  full_join(meta_filter, by = c("campaign", "kit_id", "transect_location"))  %>%
  # add rows for samples not collected, creating a "full" dataset of all possible samples
  mutate(tc_flag = case_when(collected == FALSE & is.na(carbon_weight_perc) & is.na(tc_flag) ~ "sample not collected",
                             notes == "kit compromised" ~ "kit compromised",
                             notes == "sample compromised" ~ "sample compromised",
                             TRUE ~ tc_flag),
         tn_flag = case_when(collected == FALSE & is.na(nitrogen_weight_perc) & is.na(tn_flag) ~ "sample not collected",
                             notes == "kit compromised" ~ "kit compromised",
                             notes == "sample compromised" ~ "sample compromised",
                             TRUE ~ tn_flag),
         carbon_weight_perc = case_when(notes == "kit compromised" ~ NA,
                                        notes == "sample compromised" ~ NA,
                                        TRUE ~ carbon_weight_perc),
         nitrogen_weight_perc = case_when(notes == "kit compromised" ~ NA,
                                          notes == "sample compromised" ~ NA,
                                          TRUE ~ nitrogen_weight_perc)) %>% 
  select(-c(sample_type, sample_method, collected, notes)) -> tctn_full