Added C. freundii complex and Y. pseudotuberculosis complex

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.0.0.9044
+Version: 2.0.0.9045
 Date: 2023-07-14
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,9 +1,10 @@
-# AMR 2.0.0.9044
+# AMR 2.0.0.9045
 
 ## New
-* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations
+* Regarding clinical breakpoints:
-* The EUCAST dosage guideline of v13.0 has been added to the `dosage` data set
+  * Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations
-* ECOFF and animal breakpoints: the `clinical_breakpoints` data set now contains epidemiological cut-off (ECOFF) values and CLSI animal breakpoints. These two new breakpoint types can be used for MIC/disk interpretation using `as.sir(..., breakpoint_type = "ECOFF")` or`as.sir(..., breakpoint_type = "animal")`, which is an important new addition for veterinary microbiology.
+  * The EUCAST dosage guideline of v13.0 has been added to the `dosage` data set
+  * The `clinical_breakpoints` data set now also contains epidemiological cut-off (ECOFF) values and CLSI animal breakpoints. These two new breakpoint types can be used for MIC/disk interpretation using `as.sir(..., breakpoint_type = "ECOFF")` or`as.sir(..., breakpoint_type = "animal")`, which is an important new addition for veterinary microbiology.
 * Added support for 30 species groups / complexes. They are gathered in a new data set `microorganisms.groups` and are used in clinical breakpoint interpretation. For example, CLSI 2023 contains breakpoints for the RGM group (Rapidly Growing Mycobacterium, containing over 80 species) which is now supported by our package.
 * Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set
   * Added `mo_oxygen_tolerance()` to retrieve the values

R/zzz.R

@@ -185,7 +185,7 @@ if (pkg_is_available("cli")) {
     try(loadNamespace("tibble"), silent = TRUE)
   }
 
-  # reference data - they have additional to improve algorithm speed
+  # reference data - they have additional data to improve algorithm speed
   # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
   AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
   AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)

data-raw/microorganisms.groups.md5

@@ -1 +1 @@
-139101675d9192fa112aa120b3da97e9
+c296aff21039582a1c2d3c092ccf848c

data-raw/microorganisms.groups.txt

@@ -83,6 +83,14 @@
 "B_CTRBC_AMLN-C"	"B_CTRBC_AMLN"	"Citrobacter amalonaticus complex"	"Citrobacter amalonaticus"
 "B_CTRBC_AMLN-C"	"B_CTRBC_FRMR"	"Citrobacter amalonaticus complex"	"Citrobacter farmeri"
 "B_CTRBC_AMLN-C"	"B_CTRBC_SDLK"	"Citrobacter amalonaticus complex"	"Citrobacter sedlakii"
+"B_CTRBC_FRND-C"	"B_CTRBC_BRAK"	"Citrobacter freundii complex"	"Citrobacter braakii"
+"B_CTRBC_FRND-C"	"B_CTRBC_FRND"	"Citrobacter freundii complex"	"Citrobacter freundii"
+"B_CTRBC_FRND-C"	"B_CTRBC_GLLN"	"Citrobacter freundii complex"	"Citrobacter gillenii"
+"B_CTRBC_FRND-C"	"B_CTRBC_MRLN"	"Citrobacter freundii complex"	"Citrobacter murliniae"
+"B_CTRBC_FRND-C"	"B_CTRBC_PRTC"	"Citrobacter freundii complex"	"Citrobacter portucalensis"
+"B_CTRBC_FRND-C"	"B_CTRBC_SDLK"	"Citrobacter freundii complex"	"Citrobacter sedlakii"
+"B_CTRBC_FRND-C"	"B_CTRBC_WRKM"	"Citrobacter freundii complex"	"Citrobacter werkmanii"
+"B_CTRBC_FRND-C"	"B_CTRBC_YONG"	"Citrobacter freundii complex"	"Citrobacter youngae"
 "B_STPHY_CONS"	"B_STPHY_ARGN"	"Coagulase-negative Staphylococcus (CoNS)"	"Staphylococcus argensis"
 "B_STPHY_CONS"	"B_STPHY_ARLT"	"Coagulase-negative Staphylococcus (CoNS)"	"Staphylococcus arlettae"
 "B_STPHY_CONS"	"B_STPHY_ARCL"	"Coagulase-negative Staphylococcus (CoNS)"	"Staphylococcus auricularis"
@@ -506,3 +514,9 @@
 "B_STRPT_VIRI"	"B_STRPT_SUIS"	"Viridans Group Streptococcus (VGS)"	"Streptococcus suis"
 "B_STRPT_VIRI"	"B_STRPT_UBRS"	"Viridans Group Streptococcus (VGS)"	"Streptococcus uberis"
 "B_STRPT_VIRI"	"B_STRPT_VSTB"	"Viridans Group Streptococcus (VGS)"	"Streptococcus vestibularis"
+"B_YERSN_PSDT-C"	"B_YERSN_PSTS"	"Yersinia pseudotuberculosis complex"	"Yersinia pestis"
+"B_YERSN_PSDT-C"	"B_YERSN_PSDT"	"Yersinia pseudotuberculosis complex"	"Yersinia pseudotuberculosis"
+"B_YERSN_PSDT-C"	"B_YERSN_PSDT_PSTS"	"Yersinia pseudotuberculosis complex"	"Yersinia pseudotuberculosis pestis"
+"B_YERSN_PSDT-C"	"B_YERSN_PSDT_PSDT"	"Yersinia pseudotuberculosis complex"	"Yersinia pseudotuberculosis pseudotuberculosis"
+"B_YERSN_PSDT-C"	"B_YERSN_SMLS"	"Yersinia pseudotuberculosis complex"	"Yersinia similis"
+"B_YERSN_PSDT-C"	"B_YERSN_WTRS"	"Yersinia pseudotuberculosis complex"	"Yersinia wautersii"

data-raw/microorganisms.md5

@@ -1 +1 @@
-fb5a6892877b6ac86040e1f0508486c5
+a79ae177d6b45404514789f45ba0f963

data-raw/microorganisms.txt

@@ -11206,6 +11206,7 @@
 "B_CTRBC_ERPS"	"Citrobacter europaeus"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"europaeus"	""	"species"	"Ribeiro et al., 2017"	"facultative anaerobe"	"LPSN"	"795042"	"515376"		"9554238"	"11150190"		1.5	""
 "B_CTRBC_FRMR"	"Citrobacter farmeri"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"farmeri"	""	"species"	"Brenner et al., 1993"	"aerobe"	"LPSN"	"774746"	"515376"		"3221799"	"11150190"		1	"1089701000112106,114263005"
 "B_CTRBC_FRND"	"Citrobacter freundii"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"freundii"	""	"species"	"Werkman et al., 1932"	"aerobe"	"LPSN"	"774747"	"515376"		"10732598"	"11150190"		1	"1089901000112108,6265002,721909006,715206000"
+"B_CTRBC_FRND-C"	"Citrobacter freundii complex"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"freundii complex"	""	"species group"		"aerobe"	"manually added"		"515376"			"11150190"		1	""
 "B_CTRBC_GLLN"	"Citrobacter gillenii"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"gillenii"	""	"species"	"Brenner et al., 2000"	"aerobe"	"LPSN"	"774750"	"515376"		"3221794"	"11150190"		1.5	"416990006"
 "B_CTRBC_KOSR"	"Citrobacter koseri"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"koseri"	""	"species"	"Frederiksen, 1970"	"aerobe"	"LPSN"	"774752"	"515376"		"3221790"	"11150190"		1	"1090401000112109,114264004"
 "B_CTRBC_MLNT"	"Citrobacter malonatica"	"synonym"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Citrobacter"	"malonatica"	""	"species"	"Young et al., 1971"	"aerobe"	"GBIF"				"5427569"	"11150190"	"3221790"	1	""
@@ -38966,6 +38967,7 @@
 "B_RPHDP_SBRC"	"Raphidiopsis subrecta"	"synonym"	"Bacteria"	"Cyanobacteria"	"Cyanobacteriia"	"Cyanobacteriales"	"Nostocaceae"	"Raphidiopsis"	"subrecta"	""	"species"	"Fremy et al."		"GBIF"				"7555557"	"3219380"	"4306613"	2	""
 "B_RPDTH"	"Rapidithrix"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Flammeovirgaceae"	"Rapidithrix"	""	""	"genus"	"Srisukchayakul et al., 2007"	"aerobe"	"LPSN"	"517677"	"522"		"4903792"			2	""
 "B_RPDTH_THLN"	"Rapidithrix thailandica"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Flammeovirgaceae"	"Rapidithrix"	"thailandica"	""	"species"	"Srisukchayakul et al., 2007"	"aerobe"	"LPSN"	"786823"	"517677"		"5917946"	"4903792"		2	""
+"B_MYCBC_RGM"	"Rapidly growing Mycobacterium (RGM)"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"rapidly growing"	""	"species group"		"facultative anaerobe"	"manually added"		"912"			"8084"		1	""
 "B_RPPPR"	"Rappaport"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Cardiobacteriales"	"Cardiobacteriaceae"	"Rappaport"	""	""	"genus"			"GBIF"				"10714677"	"8970"		2	""
 "B_RPPPR_ISRL"	"Rappaport israeli"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Cardiobacteriales"	"Cardiobacteriaceae"	"Rappaport"	"israeli"	""	"species"			"GBIF"				"10890221"	"10714677"		2	""
 "B_RRGLB"	"Rariglobus"	"accepted"	"Bacteria"	"Verrucomicrobiota"	"Opitutae"	"Opitutales"	"Opitutaceae"	"Rariglobus"	""	""	"genus"	"Pitt et al., 2020"		"LPSN"	"4967"	"993"		"11151485"			2	""
@@ -51989,6 +51991,7 @@
 "B_YERSN_PHLM"	"Yersinia philomiragia"	"synonym"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"philomiragia"	""	"species"	"Jensen et al., 1969"	"microaerophile"	"LPSN"	"783201"	"516947"	"776319"				1	""
 "B_YERSN_PRXM"	"Yersinia proxima"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"proxima"	""	"species"	"Le Guern et al., 2020"	"likely facultative anaerobe"	"LPSN"	"14095"	"516947"					1.5	""
 "B_YERSN_PSDT"	"Yersinia pseudotuberculosis"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"pseudotuberculosis"	""	"species"	"Smith et al., 1965"	"likely facultative anaerobe"	"LPSN"	"783202"	"516947"		"5427620"	"3221889"	"5427631"	1	"90530002"
+"B_YERSN_PSDT-C"	"Yersinia pseudotuberculosis complex"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"pseudotuberculosis complex"	""	"species group"		"likely facultative anaerobe"	"manually added"		"516947"			"3221889"		1	""
 "B_YERSN_PSDT_PSTS"	"Yersinia pseudotuberculosis pestis"	"synonym"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"pseudotuberculosis"	"pestis"	"subspecies"	"Bercovier et al., 1981"	"aerobe"	"LPSN"	"798529"	"783202"	"785226"				1	""
 "B_YERSN_PSDT_PSDT"	"Yersinia pseudotuberculosis pseudotuberculosis"	"synonym"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"pseudotuberculosis"	"pseudotuberculosis"	"subspecies"	"Bercovier et al., 1981"	"aerobe"	"LPSN"	"798530"	"783202"	"783202"				1	""
 "B_YERSN_RCHS"	"Yersinia rochesterensis"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Yersiniaceae"	"Yersinia"	"rochesterensis"	""	"species"	"Nguyen et al., 2021"	"likely facultative anaerobe"	"LPSN"	"17336"	"516947"		"11652009"	"3221889"		1.5	""
@@ -52167,4 +52170,3 @@
 "B_ZYMPH"	"Zymophilus"	"synonym"	"Bacteria"	"Bacillota"	"Negativicutes"	"Selenomonadales"	"Selenomonadaceae"	"Zymophilus"	""	""	"genus"	"Schleifer et al., 1990"	"anaerobe"	"LPSN"	"516961"	"2042"	"516396"				2	"438883001"
 "B_ZYMPH_PCVR"	"Zymophilus paucivorans"	"synonym"	"Bacteria"	"Bacillota"	"Negativicutes"	"Selenomonadales"	"Selenomonadaceae"	"Zymophilus"	"paucivorans"	""	"species"	"Schleifer et al., 1990"	"anaerobe"	"LPSN"	"783229"	"516961"	"792213"				2	"440843008"
 "B_ZYMPH_RFFN"	"Zymophilus raffinosivorans"	"synonym"	"Bacteria"	"Bacillota"	"Negativicutes"	"Selenomonadales"	"Selenomonadaceae"	"Zymophilus"	"raffinosivorans"	""	"species"	"Schleifer et al., 1990"	"anaerobe"	"LPSN"	"783230"	"516961"	"792212"				2	"440844002"
-"B_MYCBC_RGM"	"Rapidly growing Mycobacterium (RGM)"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"rapidly growing"	""	"species group"		"facultative anaerobe"	"manually added"		"912"			"8084"		1	""

data-raw/reproduction_of_microorganisms.groups.R

@@ -38,6 +38,13 @@ devtools::load_all()
 # Install the WHONET software on Windows (http://www.whonet.org/software.html),
 # and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
 
+
+# BACTERIAL COMPLEXES
+# find all bacterial complex in the NCBI Taxonomy Browser here:
+# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=6&lin=f&keep=1&srchmode=1&unlock
+# and search the page for 'complex', then follow the link and add the missing ones in this R file
+
+
 # READ DATA ----
 
 whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
@@ -131,6 +138,16 @@ microorganisms.groups <- whonet_organisms %>%
   bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Eikenella corrodens", keep_synonyms = TRUE))) %>%
   bind_rows(tibble(mo_group = as.mo("HACEK"), mo = microorganisms %>% filter(genus == "Kingella") %>% pull(mo))) %>%
   bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Actinobacillus actinomycetemcomitans", keep_synonyms = TRUE))) %>%
+  # Citrobacter freundii complex in the NCBI Taxonomy Browser:
+  # https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1344959
+  filter(mo_group != "B_CTRBC_FRND-C") %>% 
+  bind_rows(tibble(mo_group = as.mo("B_CTRBC_FRND-C"),
+                   mo = paste("Citrobacter", c("freundii", "braakii", "gillenii", "murliniae", "portucalensis", "sedlakii", "werkmanii", "youngae")) %>% as.mo(keep_synonyms = TRUE))) %>% 
+  # Yersinia pseudotuberculosis complex in the NCBI Taxonomy Browser:
+  # https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1649845
+  filter(mo_group != "B_YERSN_PSDT-C") %>% 
+  bind_rows(tibble(mo_group = as.mo("B_YERSN_PSDT-C"),
+                   mo = paste("Yersinia", c("pseudotuberculosis", "pestis", "similis", "wautersii")) %>% as.mo(keep_synonyms = TRUE))) %>% 
   # RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
   filter(mo_group != "B_MYCBC_RGM") %>% 
   bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),

man/microorganisms.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data Set with 52 169 Microorganisms}
+\title{Data Set with 52 171 Microorganisms}
 \format{
-A \link[tibble:tibble]{tibble} with 52 169 observations and 23 variables:
+A \link[tibble:tibble]{tibble} with 52 171 observations and 23 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package. \emph{This is a unique identifier.}
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. \emph{This is a unique identifier.}
@@ -14,7 +14,7 @@ A \link[tibble:tibble]{tibble} with 52 169 observations and 23 variables:
 \item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}
 \item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters, e.g. "Váňová" becomes "Vanova".
 \item \code{lpsn}\cr Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, \emph{Acetobacter ascendens} has LPSN Record number 7864 and 11011. Only the first is available in the \code{microorganisms} data set.
-\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4\% of all ~36 000 bacteria in the data set contain an oxygen tolerance.
+\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4\% of all ~37 000 bacteria in the data set contain an oxygen tolerance.
 \item \code{lpsn_parent}\cr LPSN identifier of the parent taxon
 \item \code{lpsn_renamed_to}\cr LPSN identifier of the currently valid taxon
 \item \code{gbif}\cr Identifier ('taxonID') of the Global Biodiversity Information Facility (GBIF)
@@ -50,7 +50,7 @@ For example, \emph{Staphylococcus pettenkoferi} was described for the first time
 
 Included taxonomic data are:
 \itemize{
-\item All ~36 000 (sub)species from the kingdoms of Archaea and Bacteria
+\item All ~37 000 (sub)species from the kingdoms of Archaea and Bacteria
 \item ~7 900 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
 \item ~5 100 (sub)species from the kingdom of Protozoa
 \item ~1 400 (sub)species from 43 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
@@ -64,7 +64,7 @@ Included taxonomic data are:
 For convenience, some entries were added manually:
 \itemize{
 \item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H
-\item 34 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
+\item 36 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
 \item 1 entry of \emph{Blastocystis} (\emph{B.  hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
 \item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
 \item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)

man/microorganisms.groups.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms.groups}
 \alias{microorganisms.groups}
-\title{Data Set with 507 Microorganisms In Species Groups}
+\title{Data Set with 521 Microorganisms In Species Groups}
 \format{
-A \link[tibble:tibble]{tibble} with 507 observations and 4 variables:
+A \link[tibble:tibble]{tibble} with 521 observations and 4 variables:
 \itemize{
 \item \code{mo_group}\cr ID of the species group / microbiological complex
 \item \code{mo}\cr ID of the microorganism belonging in the species group / microbiological complex

tests/tinytest.R

@@ -67,8 +67,8 @@ if (tryCatch(isTRUE(AMR:::import_fn("isJob", "rstudioapi")()), error = function(
 
     # start the unit tests
     suppressMessages(
-      out <- run_test_dir(
+      out <- test_package("AMR",
-        ifelse(dir.exists("inst/tinytest"),
+        testdir = ifelse(dir.exists("inst/tinytest"),
           "inst/tinytest",
           "tinytest"
         ),