fix `mo_rank()` for 'unknown' MOs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.0.0.9011
-Date: 2023-04-19
+Version: 2.0.0.9012
+Date: 2023-04-20
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,9 +1,10 @@
-# AMR 2.0.0.9011
+# AMR 2.0.0.9012
 
 ## Changed
 * formatting fix for `sir_interpretation_history()`
 * Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
 * Added microbial codes for Gram-negative/positive anaerobic bacteria
+* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
 
 
 # AMR 2.0.0

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,

man/AMR.Rd

@@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
 
 This work was published in the Journal of Statistical Software (Volume 104(3); \doi{jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
 
-After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
+After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated December 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
 
 The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
 }