step 2: classify duration - how to deal with the not specified values

[aylapear]

The chronic and acute rules have gaps which causes many values to be coded as not specified.

Currently these values are being filtered out.

It has been mentioned that these should be classified as acute instead of being remove but waiting on confirmation of this.

[aylapear]

  data_classified <- data |>
    dplyr::mutate(
      duration_class = dplyr::case_when(
        # Fish and Amphibians
        stringr::str_detect(ecological_group, "(?i)^amphibian$|^fish$")  & obs_duration_mean_std <= 96 ~ "acute",
        stringr::str_detect(ecological_group, "(?i)^amphibian$|^fish$") & stringr::str_detect(simple_lifestage, "(?i)^juvenile$|(?i)^adult$")  & obs_duration_mean_std >= 504 ~ "chronic",
        stringr::str_detect(ecological_group, "(?i)^amphibian$|^fish$") & stringr::str_detect(simple_lifestage, "(?i)^els$")  & obs_duration_mean_std >= 168 ~ "chronic",
        # Invertebrates
        stringr::str_detect(ecological_group, "(?i)^invertebrate$") & obs_duration_mean_std <= 96 ~ "acute",
        stringr::str_detect(ecological_group, "(?i)^invertebrate$") & stringr::str_detect(ecological_group_class, "(?i)Planktonic Invertebrate") & obs_duration_mean_std > 96 ~ "chronic",
        stringr::str_detect(ecological_group, "(?i)^invertebrate$") & stringr::str_detect(ecological_group_class, "(?i)Regular") & obs_duration_mean_std >= 168 ~ "chronic",
        # Algae
        stringr::str_detect(ecological_group, "(?i)^algae$") & obs_duration_mean_std <= 24 ~ "acute",
        stringr::str_detect(ecological_group, "(?i)^algae$") & obs_duration_mean_std > 24 ~ "chronic",
        # Plants
        stringr::str_detect(ecological_group, "(?i)^plant$") & obs_duration_mean_std <= 48 ~ "acute",
        stringr::str_detect(ecological_group, "(?i)^plant$") & obs_duration_mean_std > 168 ~ "chronic",
        TRUE ~ "not specified"
      ) 
    ) |>
    dplyr::filter(!(duration_class == "not specified"))

The last line can be switched to have things turn to acute if they don't meet any of the other rules.

[aylapear]

They have been set to acute and tested