fix mo_rank() for 'unknown' MOs

data-raw/clin_break.md5

@@ -1 +1 @@
-ad4649f72b21de1c1828c0686c754f20
+0a9ea3545d68b95108a28096d975388f

data-raw/microorganisms.md5

@@ -1 +1 @@
-aec0e9d495ebee3079f9aab766d7a38f
+20bb7a68431826bce777a6c239f0fed0

data-raw/microorganisms.txt

@@ -1,12 +1,12 @@
 "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	""

data-raw/reproduction_of_clinical_breakpoints.R

@@ -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,