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new species groups, updated clinical breakpoints

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dr. M.S. (Matthijs) Berends
2023-07-08 17:30:05 +02:00
parent 2d97cca6d9
commit acb534102b
172 changed files with 44445 additions and 52835 deletions
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18
data-raw/species groups.R Normal file
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g <- certetoolbox::import_clipboard()
g <- g %>% as_tibble()
g
for (i in seq_len(nrow(g))) {
if (is.na(g$taxonomy_from[i])) next
mo <- as.mo(g$taxonomy_from[i])
g$phylum[i] <- mo_phylum(mo)
g$class[i] <- mo_class(mo)
g$order[i] <- mo_order(mo)
g$family[i] <- mo_family(mo)
g$genus[i] <- mo_genus(mo)
g$species[i] <- paste(mo_species(mo), "complex")
g$lpsn_parent[i] <- mo_property(mo, property = "lpsn_parent")
g$gbif_parent[i] <- mo_property(mo, property = "gbif_parent")
g$oxygen_tolerance[i] <- mo_property(mo, property = "oxygen_tolerance")
g$prevalence[i] <- mo_property(mo, property = "prevalence")
}
certetoolbox::export_clipboard(g)