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fix mo_rank() for 'unknown' MOs

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dr. M.S. (Matthijs) Berends
2023-04-20 15:20:41 +02:00
parent 2758615cd0
commit 9148a2dcf4
25 changed files with 1270 additions and 1268 deletions
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data-raw/clin_break.md5
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data-raw/clinical_breakpoints.txt
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data-raw/microorganisms.txt
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"mo" "fullname" "status" "kingdom" "phylum" "class" "order" "family" "genus" "species" "subspecies" "rank" "ref" "source" "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" "gbif_renamed_to" "prevalence" "snomed"
"B_ANAER" "(unknown anaerobic bacteria)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_ANAER-NEG" "(unknown anaerobic Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_ANAER-POS" "(unknown anaerobic Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"F_FUNGUS" "(unknown fungus)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMN" "(unknown Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMP" "(unknown Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-positives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"UNKNOWN" "(unknown name)" "accepted" "(unknown kingdom)" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"F_YEAST" "(unknown yeast)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_ANAER" "(unknown anaerobic bacteria)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"B_ANAER-NEG" "(unknown anaerobic Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"B_ANAER-POS" "(unknown anaerobic Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"F_FUNGUS" "(unknown fungus)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"B_GRAMN" "(unknown Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"B_GRAMP" "(unknown Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"UNKNOWN" "(unknown name)" "accepted" "(unknown kingdom)" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"F_YEAST" "(unknown yeast)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "manually added" 2 ""
"B_[FAM]_ABDTBCTR" "Abditibacteriaceae" "accepted" "Bacteria" "Abditibacteriota" "Abditibacteriia" "Abditibacteriales" "Abditibacteriaceae" "" "" "" "family" "Tahon et al., 2018" "LPSN" "4812" "4982" "10678443" "10853930" 2 ""
"B_[ORD]_ABDTBCTR" "Abditibacteriales" "accepted" "Bacteria" "Abditibacteriota" "Abditibacteriia" "Abditibacteriales" "" "" "" "" "order" "Tahon et al., 2018" "LPSN" "4982" "29679" "10853930" 2 ""
"B_[CLS]_ADTBCTRA" "Abditibacteriia" "accepted" "Bacteria" "Abditibacteriota" "Abditibacteriia" "" "" "" "" "" "class" "Tahon et al., 2018" "LPSN" "29679" "774" 2 ""

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data-raw/reproduction_of_clinical_breakpoints.R
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@@ -178,6 +178,7 @@ breakpoints_new <- breakpoints %>%
site = gsub(".*(UTI|urinary|urine).*", "UTI", SITE_OF_INFECTION, ignore.case = TRUE),
mo,
rank_index = case_when(
is.na(mo_rank(mo)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
mo_rank(mo) %like% "(infra|sub)" ~ 1,
mo_rank(mo) == "species" ~ 2,
mo_rank(mo) == "genus" ~ 3,