library(dplyr)
library(seabirdPrey)
# read-manual-corrections ----
## read-in-raw-prey-taxonomy ----
seabirddiet <- readr::read_csv(here::here("data-raw", "intermediate", "seabirddiet.csv"),
guess_max = Inf, na = c("", "NA"))
# read in and post process manual corrections
ref_manual <- readr::read_csv(here::here("data-raw",
"manual_corrections",
"reference_manual_clean.csv")) %>%
# get rid of long hyphen
mutate(rename = stringr::str_replace(rename, "–", "-")) %>%
# get rid of trailing .
mutate(rename = stringr::str_replace(rename, "\\.$", "")) %>%
# fuzzy match missing references in seabirddiet to ref_manual
ref_bind_matched_missing_manual(seabirddiet, .)
missing <- ref_find_missing_manual(seabirddiet, ref_manual)
#inspect missing
missing
# if all good, add to ref_manual
#ref_add_manual(missing$reference, ref_manual)
# tidy-references ----
ref_tidy <- tidy_refs(ref_manual)
# get_ref_table ----
ref <- get_ref_tbl(ref_tidy)
# writeout-ref_table ----
ref %>%
assertr::assert(assertr::is_uniq(c("ref_valid", "ref_id"))) %>%
assertr::assert(stringr::str_detect("ref_valid", "–") == F) %>%
assertr::verify(assertr::has_all_names("ref_id", "ref_valid")) %>%
readr::write_csv(here::here("data-raw", "metadata", "references.csv"))
# get-join_ref ----
join_ref <- get_join_ref(ref_tidy, ref)
join_ref <- join_ref %>% dplyr::bind_rows(
join_ref %>%
mutate(reference = stringr::str_replace_all(reference, "–", "?"))) %>%
distinct()
# writeout-join_ref ----
join_ref %>%
# validate
assertr::assert(is.numeric("ref_n")) %>%
assertr::verify(nrow(.) == 309) %>%
assertr::assert(assertr::is_uniq, reference) %>%
assertr::verify(all(seabirddiet$reference %in% .$reference)) %>%
assertr::verify(assertr::not_na("ref_ids")) %>%
assertr::verify(assertr::has_all_names("reference", "ref_n", "ref_ids")) %>%
# write out
readr::write_csv(here::here("data-raw", "joins", "ref_join.csv"))
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