mirror of https://github.com/msberends/AMR.git
34 lines
1.1 KiB
R
34 lines
1.1 KiB
R
snomed2 <- microorganisms %>%
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filter(mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
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pull(snomed)
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new_typhi <- microorganisms %>%
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filter(mo == "B_SLMNL_THSS") %>%
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slice(c(1, 1, 1)) %>%
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mutate(
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mo = c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY"),
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fullname = c("Salmonella Typhi", "Salmonella Typhimurium", "Salmonella Paratyphi"),
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subspecies = c("Typhi", "Typhimurium", "Paratyphi"),
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snomed = snomed2
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)
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new_groupa <- microorganisms %>%
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filter(mo == "B_SLMNL_GRPB") %>%
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mutate(
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mo = "B_SLMNL_GRPA",
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fullname = gsub("roup B", "roup A", fullname),
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species = gsub("roup B", "roup A", species)
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)
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microorganisms$mo <- as.character(microorganisms$mo)
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microorganisms <- microorganisms %>%
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filter(!mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
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bind_rows(new_typhi, new_groupa) %>%
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arrange(fullname)
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microorganisms$lpsn_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "516547"
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microorganisms$gbif_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "3221815"
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class(microorganisms$mo) <- c("mo", "character")
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