(v1.7.1.9056) unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.7.1.9055
+Version: 1.7.1.9056
 Date: 2021-11-29
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9055
+# `AMR` 1.7.1.9056
 ## <small>Last updated: 29 November 2021</small>
 
 ### Breaking changes
@@ -55,6 +55,7 @@
 * The `proportion_df()`, `count_df()` and `rsi_df()` functions now return with the additional S3 class 'rsi_df' so they can be extended by other packages
 * The `mdro()` function now returns `NA` for all rows that have no test results
 * The `species_id` column in the `microorganisms` data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and `mo_url()` has been updated to reflect this change.
+* Fixed a small bug in the functions `get_episode()` and `is_new_episode()`
 
 ### Other
 * This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.

R/episode.R

@@ -27,7 +27,7 @@
 #' 
 #' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode.
 #' @inheritSection lifecycle Stable Lifecycle
-#' @param x vector of dates (class `Date` or `POSIXt`)
+#' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
 #' @param episode_days required episode length in days, can also be less than a day or `Inf`, see *Details*
 #' @param ... ignored, only in place to allow future extensions
 #' @details 
@@ -182,5 +182,5 @@ exec_episode <- function(x, type, episode_days, ...) {
   }
   
   ord <- order(x)
-  run_episodes(x[ord], episode_seconds)[ord]
+  run_episodes(x[ord], episode_seconds)[order(ord)]
 }

data-raw/microorganisms.txt

@@ -2526,9 +2526,7 @@
 "B_AEQRV"	"Aequorivita"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	""	""	"genus"	""	515048	"LPSN"	3	"427000006"
 "B_AEQRV_AEST"	"Aequorivita aestuarii"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"aestuarii"	""	"species"	"Hahnke et al., 2017"	795331	"LPSN"	3	"character(0)"
 "B_AEQRV_ANTR"	"Aequorivita antarctica"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"antarctica"	""	"species"	"Bowman et al., 2002"	772870	"LPSN"	3	"425986000"
-"B_AEQRV_AQMR"	"Aequorivita aquimaris"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"aquimaris"	""	"species"	"Garcia-Lopez et al., 2020"	7810	"LPSN"	3	"character(0)"
 "B_AEQRV_AQMR"	"Aequorivita aquimaris"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"aquimaris"	""	"species"	"Garcia-Lopez et al., 2020"	240	"LPSN"	3	"character(0)"
-"B_AEQRV_AQMR"	"Aequorivita aquimaris"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"aquimaris"	""	"species"	"Garcia-Lopez et al., 2020"	10522	"LPSN"	3	"character(0)"
 "B_AEQRV_CPSS"	"Aequorivita capsosiphonis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"capsosiphonis"	""	"species"	"Park et al., 2009"	787769	"LPSN"	3	"character(0)"
 "B_AEQRV_CROC"	"Aequorivita crocea"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"crocea"	""	"species"	"Bowman et al., 2002"	772871	"LPSN"	3	"427267004"
 "B_AEQRV_ECHN"	"Aequorivita echinoideorum"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"echinoideorum"	""	"species"	"Hahnke et al., 2017"	795332	"LPSN"	3	"character(0)"
@@ -2539,7 +2537,6 @@
 "B_AEQRV_SSKK"	"Aequorivita soesokkakensis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"soesokkakensis"	""	"species"	"Hahnke et al., 2017"	795334	"LPSN"	3	"character(0)"
 "B_AEQRV_SBLT"	"Aequorivita sublithincola"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"sublithincola"	""	"species"	"Bowman et al., 2002"	772873	"LPSN"	3	"426358009"
 "B_AEQRV_TDRD"	"Aequorivita todarodis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"todarodis"	""	"species"	"Zhang et al., 2020"	1653	"LPSN"	3	"character(0)"
-"B_AEQRV_TDRD"	"Aequorivita todarodis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"todarodis"	""	"species"	"Zhang et al., 2020"	7480	"LPSN"	3	"character(0)"
 "B_AEQRV_VSCS"	"Aequorivita viscosa"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"viscosa"	""	"species"	"Liu et al., 2013"	791065	"LPSN"	3	"character(0)"
 "B_AEQRV_VLDV"	"Aequorivita vladivostokensis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aequorivita"	"vladivostokensis"	""	"species"	"Hahnke et al., 2017"	795335	"LPSN"	3	"character(0)"
 "B_AERBC"	"Aeribacillus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Caryophanales"	"Bacillaceae"	"Aeribacillus"	""	""	"genus"	""	517994	"LPSN"	2	"771465008"
@@ -10655,9 +10652,7 @@
 "C_BCHNR_WRGH_CLRN"	"Buchnerina wrightiana clarioniana"	"Chromista"	"Foraminifera"	"(unknown class)"	"Lagenida"	"Ellipsolagenidae"	"Buchnerina"	"wrightiana"	"clarioniana"	"infraspecies"	"McCulloch, 1977"		"CoL"	3	"character(0)"
 "C_BCHNR_YKYM"	"Buchnerina yokoyamae"	"Chromista"	"Foraminifera"	"(unknown class)"	"Lagenida"	"Ellipsolagenidae"	"Buchnerina"	"yokoyamae"	""	"species"	"Millett, 1895"		"CoL"	3	"character(0)"
 "B_BUDVC"	"Budvicia"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Budviciaceae"	"Budvicia"	""	""	"genus"	""	4094	"LPSN"	1	"55851000"
-"B_BUDVC"	"Budvicia"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Budviciaceae"	"Budvicia"	""	""	"genus"	""	515277	"LPSN"	1	"55851000"
 "B_BUDVC_AQTC"	"Budvicia aquatica"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Budviciaceae"	"Budvicia"	"aquatica"	""	"species"	"Bouvet et al., 1985"	7142	"LPSN"	1	"75464008"
-"B_BUDVC_AQTC"	"Budvicia aquatica"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Budviciaceae"	"Budvicia"	"aquatica"	""	"species"	"Bouvet et al., 1985"	774260	"LPSN"	1	"75464008"
 "B_BUDVC_DPLP"	"Budvicia diplopodorum"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Budviciaceae"	"Budvicia"	"diplopodorum"	""	"species"	"Lang et al., 2013"	790413	"LPSN"	1	"character(0)"
 "B_[FAM]_BUDVICIC"	"Budviciaceae"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Budviciaceae"	""	""	""	"family"	"Adeolu et al., 2016"		"manually added"	1	"character(0)"
 "C_BHRNG"	"Buehringa"	"Chromista"	"Ciliophora"	"Oligotrichea"	"Strombidiida"	"Strombidiidae"	"Buehringa"	""	""	"genus"	""		"CoL"	3	"character(0)"
@@ -10870,7 +10865,6 @@
 "B_BRKHL_VRNS"	"Burkholderia pseudomultivorans"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"pseudomultivorans"	""	"species"	"Peeters et al., 2014"	791434	"LPSN"	2	"character(0)"
 "B_BRKHL_PURQ"	"Burkholderia puraquae"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"puraquae"	""	"species"	"Martina et al., 2018"	796421	"LPSN"	2	"character(0)"
 "B_BRKHL_PYRR"	"Burkholderia pyrrocinia"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"pyrrocinia"	""	"species"	"Vandamme et al., 2004"	7158	"LPSN"	2	"113677007"
-"B_BRKHL_PYRR"	"Burkholderia pyrrocinia"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"pyrrocinia"	""	"species"	"Vandamme et al., 2004"	774298	"LPSN"	2	"113677007"
 "B_BRKHL_SMNL"	"Burkholderia seminalis"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"seminalis"	""	"species"	"Vanlaere et al., 2008"	787432	"LPSN"	2	"3441000146100"
 "B_BRKHL_SNGL"	"Burkholderia singularis"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"singularis"	""	"species"	"Vandamme et al., 2017"	796265	"LPSN"	2	"character(0)"
 "B_BRKHL_STBL"	"Burkholderia stabilis"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Burkholderiaceae"	"Burkholderia"	"stabilis"	""	"species"	"Vandamme et al., 2000"	774304	"LPSN"	2	"416616001"
@@ -14884,7 +14878,6 @@
 "F_CLVTS_TNTC"	"Clavatospora tentacula"	"Fungi"	"Ascomycota"	"Sordariomycetes"	"Microascales"	"Halosphaeriaceae"	"Clavatospora"	"tentacula"	""	"species"	"Sv Nilsson, 1964"		"CoL"	3	"character(0)"
 "B_CLVBC"	"Clavibacter"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	""	""	"genus"	""	515381	"LPSN"	2	"432467001"
 "B_CLVBC_CPSC"	"Clavibacter capsici"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"capsici"	""	"species"	"Li et al., 2018"	7145	"LPSN"	2	"character(0)"
-"B_CLVBC_CPSC"	"Clavibacter capsici"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"capsici"	""	"species"	"Li et al., 2018"	798782	"LPSN"	2	"character(0)"
 "B_CLVBC_INSD"	"Clavibacter insidiosus"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"insidiosus"	""	"species"	"Li et al., 2018"	798137	"LPSN"	2	"character(0)"
 "B_CLVBC_MCHG"	"Clavibacter michiganensis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"michiganensis"	""	"species"	"Davis et al., 1984"	783651	"LPSN"	2	"434065004"
 "B_CLVBC_MCHG_CLFR"	"Clavibacter michiganensis californiensis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"michiganensis"	"californiensis"	"species"	"Yasuhara-Bell et al., 2015"	792619	"LPSN"	2	"character(0)"
@@ -14892,9 +14885,7 @@
 "B_CLVBC_MCHG_MCHG"	"Clavibacter michiganensis michiganensis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"michiganensis"	"michiganensis"	"subsp."	"Davis et al., 1984"	774773	"LPSN"	2	"434699002"
 "B_CLVBC_MCHG_PHSL"	"Clavibacter michiganensis phaseoli"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"michiganensis"	"phaseoli"	"species"	"Gonzalez et al., 2014"	791833	"LPSN"	2	"character(0)"
 "B_CLVBC_NBRS"	"Clavibacter nebraskensis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"nebraskensis"	""	"species"	"Li et al., 2018"	7143	"LPSN"	2	"character(0)"
-"B_CLVBC_NBRS"	"Clavibacter nebraskensis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"nebraskensis"	""	"species"	"Li et al., 2018"	798139	"LPSN"	2	"character(0)"
 "B_CLVBC_SPDN"	"Clavibacter sepedonicus"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"sepedonicus"	""	"species"	"Li et al., 2018"	7144	"LPSN"	2	"character(0)"
-"B_CLVBC_SPDN"	"Clavibacter sepedonicus"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"sepedonicus"	""	"species"	"Li et al., 2018"	798141	"LPSN"	2	"character(0)"
 "B_CLVBC_TSSL"	"Clavibacter tessellarius"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"tessellarius"	""	"species"	"Li et al., 2018"	798142	"LPSN"	2	"character(0)"
 "B_CLVBC_ZHNG"	"Clavibacter zhangzhiyongii"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Micrococcales"	"Microbacteriaceae"	"Clavibacter"	"zhangzhiyongii"	""	"species"	"Tian et al., 2021"	19559	"LPSN"	2	"character(0)"
 "F_CLVSP"	"Clavispora"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"Metschnikowiaceae"	"Clavispora"	""	""	"genus"	""		"CoL"	3	"28615005"
@@ -15725,7 +15716,6 @@
 "B_CMPNL_PABL"	"Companilactobacillus pabuli"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"pabuli"	""	"species"	"Jung et al., 2021"	17745	"LPSN"	2	"character(0)"
 "B_CMPNL_PRLM"	"Companilactobacillus paralimentarius"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"paralimentarius"	""	"species"	"Zheng et al., 2020"	10797	"LPSN"	2	"character(0)"
 "B_CMPNL_SLSC"	"Companilactobacillus salsicarnum"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"salsicarnum"	""	"species"	"Zheng et al., 2020"	10719	"LPSN"	2	"character(0)"
-"B_CMPNL_SNTS"	"Companilactobacillus suantsaicola"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"suantsaicola"	""	"species"	"Zheng et al., 2020"	18766	"LPSN"	2	"character(0)"
 "B_CMPNL_SNTS"	"Companilactobacillus suantsaicola"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"suantsaicola"	""	"species"	"Zheng et al., 2020"	12970	"LPSN"	2	"character(0)"
 "B_CMPNL_TCCT"	"Companilactobacillus tucceti"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"tucceti"	""	"species"	"Zheng et al., 2020"	10821	"LPSN"	2	"character(0)"
 "B_CMPNL_VRSM"	"Companilactobacillus versmoldensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Companilactobacillus"	"versmoldensis"	""	"species"	"Zheng et al., 2020"	10825	"LPSN"	2	"character(0)"
@@ -20814,10 +20804,8 @@
 "C_ELLDS_MEDS"	"Eggerelloides medius"	"Chromista"	"Foraminifera"	"Globothalamea"	"Lituolida"	"Prolixoplectidae"	"Eggerelloides"	"medius"	""	"species"	"Hoglund, 1947"		"CoL"	3	"character(0)"
 "C_ELLDS_SCBR"	"Eggerelloides scaber"	"Chromista"	"Foraminifera"	"Globothalamea"	"Lituolida"	"Prolixoplectidae"	"Eggerelloides"	"scaber"	""	"species"	"Williamson, 1858"		"CoL"	3	"character(0)"
 "C_ELLDS_SCBR_INRN"	"Eggerelloides scaber inornata"	"Chromista"	"Foraminifera"	"Globothalamea"	"Lituolida"	"Prolixoplectidae"	"Eggerelloides"	"scaber"	"inornata"	"infraspecies"	"Rhumbler, 1936"		"CoL"	3	"character(0)"
-"B_EGGRT"	"Eggerthella"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	"Eggerthella"	""	""	"genus"	""	521510	"LPSN"	2	"c(\"414079001\", \"414080003\", \"414075007\")"
 "B_EGGRT"	"Eggerthella"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	"Eggerthella"	""	""	"genus"	""	515567	"LPSN"	2	"c(\"414079001\", \"414080003\", \"414075007\")"
 "B_EGGRT_GDYN"	"Eggerthella guodeyinii"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	"Eggerthella"	"guodeyinii"	""	"species"	"Ge et al., 2021"	20102	"LPSN"	2	"character(0)"
-"B_EGGRT_LENT"	"Eggerthella lenta"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	"Eggerthella"	"lenta"	""	"species"	"Wade et al., 2008"	775884	"LPSN"	2	"414077004"
 "B_EGGRT_LENT"	"Eggerthella lenta"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	"Eggerthella"	"lenta"	""	"species"	"Wade et al., 2008"	7150	"LPSN"	2	"414077004"
 "B_EGGRT_SNNS"	"Eggerthella sinensis"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	"Eggerthella"	"sinensis"	""	"species"	"Lau et al., 2008"	785467	"LPSN"	2	"414078009"
 "B_[FAM]_EGGRTHLL"	"Eggerthellaceae"	"Bacteria"	"Actinobacteria"	"Coriobacteriia"	"Eggerthellales"	"Eggerthellaceae"	""	""	""	"family"			"CoL"	2	"770382002"
@@ -26256,7 +26244,6 @@
 "B_GORDN_ACHN"	"Gordonia aichiensis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"aichiensis"	""	"species"	"Klatte et al., 1994"	776577	"LPSN"	2	"416711002"
 "B_GORDN_ALKL"	"Gordonia alkaliphila"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"alkaliphila"	""	"species"	"Cha et al., 2013"	790425	"LPSN"	2	"character(0)"
 "B_GORDN_ALKN"	"Gordonia alkanivorans"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"alkanivorans"	""	"species"	"Kummer et al., 1999"	776578	"LPSN"	2	"432009007"
-"B_GORDN_AMAR"	"Gordonia amarae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"amarae"	""	"species"	"Klatte et al., 1994"	776579	"LPSN"	2	"432969007"
 "B_GORDN_AMAR"	"Gordonia amarae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"amarae"	""	"species"	"Klatte et al., 1994"	7149	"LPSN"	2	"432969007"
 "B_GORDN_AMCL"	"Gordonia amicalis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"amicalis"	""	"species"	"Kim et al., 2000"	776580	"LPSN"	2	"432010002"
 "B_GORDN_ARAI"	"Gordonia araii"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Gordoniaceae"	"Gordonia"	"araii"	""	"species"	"Kageyama et al., 2006"	785295	"LPSN"	2	"character(0)"
@@ -28978,13 +28965,10 @@
 "C_HHRYA_VRDS"	"Holophrya viridis"	"Chromista"	"Ciliophora"	"Prostomatea"	"Prostomatida"	"Holophryidae"	"Holophrya"	"viridis"	""	"species"	""		"CoL"	3	"character(0)"
 "C_HHRYA_VORX"	"Holophrya vorax"	"Chromista"	"Ciliophora"	"Prostomatea"	"Prostomatida"	"Holophryidae"	"Holophrya"	"vorax"	""	"species"	"Dragesco, 1960"		"CoL"	3	"character(0)"
 "C_[FAM]_HOLPHRYD"	"Holophryidae"	"Chromista"	"Ciliophora"	"Prostomatea"	"Prostomatida"	"Holophryidae"	""	""	""	"family"	""		"CoL"	2	"character(0)"
-"B_HLSPR"	"Holospora"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	""	""	"genus"	""	521511	"LPSN"	2	"432450008"
 "B_HLSPR"	"Holospora"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	""	""	"genus"	""	517251	"LPSN"	2	"432450008"
 "B_HLSPR_CRYP"	"Holospora caryophila"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	"caryophila"	""	"species"	"Preer et al., 1982"	784018	"LPSN"	2	"433982009"
 "B_HLSPR_ELGN"	"Holospora elegans"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	"elegans"	""	"species"	"Preer et al., 1982"	784019	"LPSN"	2	"434171007"
-"B_HLSPR_OBTS"	"Holospora obtusa"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	"obtusa"	""	"species"	"Gromov et al., 1981"	784020	"LPSN"	2	"434038006"
 "B_HLSPR_OBTS"	"Holospora obtusa"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	"obtusa"	""	"species"	"Gromov et al., 1981"	7154	"LPSN"	2	"434038006"
-"B_HLSPR_UNDL"	"Holospora undulata"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	"undulata"	""	"species"	"Gromov et al., 1981"	784021	"LPSN"	2	"433983004"
 "B_HLSPR_UNDL"	"Holospora undulata"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	"Holosporaceae"	"Holospora"	"undulata"	""	"species"	"Gromov et al., 1981"	7155	"LPSN"	2	"433983004"
 "B_[FAM]_HOLOSPRC"	"Holosporaceae"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Rickettsiales"	"Holosporaceae"	""	""	""	"family"	""		"CoL"	2	"414206002"
 "B_[ORD]_HOLSPRLS"	"Holosporales"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Holosporales"	""	""	""	""	"order"			"CoL"	2	"character(0)"
@@ -31349,7 +31333,6 @@
 "B_LCTPL_DWNS"	"Lactiplantibacillus daowaiensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"daowaiensis"	""	"species"	"Zheng et al., 2020"	10693	"LPSN"	2	"character(0)"
 "B_LCTPL_DNGL"	"Lactiplantibacillus dongliensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"dongliensis"	""	"species"	"Zheng et al., 2020"	10692	"LPSN"	2	"character(0)"
 "B_LCTPL_FBFR"	"Lactiplantibacillus fabifermentans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"fabifermentans"	""	"species"	"Zheng et al., 2020"	10753	"LPSN"	2	"character(0)"
-"B_LCTPL_GARI"	"Lactiplantibacillus garii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"garii"	""	"species"	"Zheng et al., 2020"	18769	"LPSN"	2	"character(0)"
 "B_LCTPL_GARI"	"Lactiplantibacillus garii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"garii"	""	"species"	"Zheng et al., 2020"	12997	"LPSN"	2	"character(0)"
 "B_LCTPL_HRBR"	"Lactiplantibacillus herbarum"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"herbarum"	""	"species"	"Zheng et al., 2020"	10861	"LPSN"	2	"character(0)"
 "B_LCTPL_MDST"	"Lactiplantibacillus modestisalitolerans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactiplantibacillus"	"modestisalitolerans"	""	"species"	"Zheng et al., 2020"	10859	"LPSN"	2	"character(0)"
@@ -33843,7 +33826,6 @@
 "B_LVLCT_SPCH"	"Levilactobacillus spicheri"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"spicheri"	""	"species"	"Zheng et al., 2020"	10816	"LPSN"	2	"character(0)"
 "B_LVLCT_SNTS"	"Levilactobacillus suantsaii"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"suantsaii"	""	"species"	"Zheng et al., 2020"	10661	"LPSN"	2	"character(0)"
 "B_LVLCT_SNTS1"	"Levilactobacillus suantsaiihabitans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"suantsaiihabitans"	""	"species"	"Zheng et al., 2020"	12998	"LPSN"	2	"character(0)"
-"B_LVLCT_SNTS1"	"Levilactobacillus suantsaiihabitans"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"suantsaiihabitans"	""	"species"	"Zheng et al., 2020"	18767	"LPSN"	2	"character(0)"
 "B_LVLCT_TNGY"	"Levilactobacillus tangyuanensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"tangyuanensis"	""	"species"	"Zheng et al., 2020"	10669	"LPSN"	2	"character(0)"
 "B_LVLCT_TNGJ"	"Levilactobacillus tongjiangensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"tongjiangensis"	""	"species"	"Zheng et al., 2020"	10667	"LPSN"	2	"character(0)"
 "B_LVLCT_WNGK"	"Levilactobacillus wangkuiensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Levilactobacillus"	"wangkuiensis"	""	"species"	"Liu et al., 2021"	20124	"LPSN"	2	"character(0)"
@@ -38985,7 +38967,6 @@
 "B_MRCMS"	"Muricomes"	"Bacteria"	"Firmicutes"	"Clostridia"	"Eubacteriales"	"Lachnospiraceae"	"Muricomes"	""	""	"genus"		518843	"LPSN"	2	"character(0)"
 "B_MRCMS_INTS"	"Muricomes intestini"	"Bacteria"	"Firmicutes"	"Clostridia"	"Eubacteriales"	"Lachnospiraceae"	"Muricomes"	"intestini"	""	"species"	"Lagkouvardos et al., 2016"	793540	"LPSN"	2	"character(0)"
 "B_MURCL"	"Muriicola"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Muriicola"	""	""	"genus"	""	7206	"LPSN"	3	"character(0)"
-"B_MURCL"	"Muriicola"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Muriicola"	""	""	"genus"	""	518000	"LPSN"	3	"character(0)"
 "B_MURCL_JJNS"	"Muriicola jejuensis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Muriicola"	"jejuensis"	""	"species"	"Kahng et al., 2010"	788644	"LPSN"	3	"character(0)"
 "B_MURCL_MRNN"	"Muriicola marianensis"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Muriicola"	"marianensis"	""	"species"	"Hu et al., 2015"	792561	"LPSN"	3	"character(0)"
 "B_MURCL_SOLI"	"Muriicola soli"	"Bacteria"	"Bacteroidetes"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Muriicola"	"soli"	""	"species"	"Kang et al., 2021"	20129	"LPSN"	3	"character(0)"
@@ -39077,12 +39058,10 @@
 "B_MYCBC_CLRF"	"Mycobacterium celeriflavum"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"celeriflavum"	""	"species"	"Shahraki et al., 2018"	792559	"LPSN"	2	"character(0)"
 "B_MYCBC_CHLN"	"Mycobacterium chelonae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chelonae"	""	"species"	"Kubica et al., 1972"	778416	"LPSN"	2	"752713421000087040"
 "B_MYCBC_CHLN_BOVS"	"Mycobacterium chelonae bovis"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chelonae"	"bovis"	"species"	"Kim et al., 2017"	796016	"LPSN"	2	"1079401000112105"
-"B_MYCBC_CHLN_CHLN"	"Mycobacterium chelonae chelonae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chelonae"	"chelonae"	"subsp."	"Kubica et al., 1972"	786944	"LPSN"	2	"character(0)"
 "B_MYCBC_CHLN_CHLN"	"Mycobacterium chelonae chelonae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chelonae"	"chelonae"	"subsp."	"Kubica et al., 1972"	9034	"LPSN"	2	"character(0)"
 "B_MYCBC_CHLN_GWNK"	"Mycobacterium chelonae gwanakae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chelonae"	"gwanakae"	"species"	"Kim et al., 2018"	797993	"LPSN"	2	"character(0)"
 "B_MYCBC_CHIT"	"Mycobacterium chitae"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chitae"	""	"species"	"Tsukamura, 1967"	778423	"LPSN"	2	"89896008"
 "B_MYCBC_CHLR"	"Mycobacterium chlorophenolicum"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chlorophenolicum"	""	"species"	"Haggblom et al., 1994"	16956	"LPSN"	2	"713611009"
-"B_MYCBC_CHLR"	"Mycobacterium chlorophenolicum"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chlorophenolicum"	""	"species"	"Haggblom et al., 1994"	778424	"LPSN"	2	"713611009"
 "B_MYCBC_CHBN"	"Mycobacterium chubuense"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"chubuense"	""	"species"	"Tsukamura, 1981"	778425	"LPSN"	2	"20498000"
 "B_MYCBC_CLMB"	"Mycobacterium colombiense"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"colombiense"	""	"species"	"Murcia et al., 2006"	785392	"LPSN"	2	"5381000146104"
 "B_MYCBC_CNCP"	"Mycobacterium conceptionense"	"Bacteria"	"Actinobacteria"	"Actinobacteria"	"Mycobacteriales"	"Mycobacteriaceae"	"Mycobacterium"	"conceptionense"	""	"species"	"Adekambi et al., 2006"	785474	"LPSN"	2	"450471003"
@@ -41367,7 +41346,6 @@
 "B_NESSR_SBFL"	"Neisseria subflava"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"subflava"	""	"species"	"Trevisan, 1889"	778639	"LPSN"	2	"77700001"
 "B_NESSR_WDSW"	"Neisseria wadsworthii"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"wadsworthii"	""	"species"	"Wolfgang et al., 2011"	789000	"LPSN"	2	"450421001"
 "B_NESSR_WEVR"	"Neisseria weaveri"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"weaveri"	""	"species"	"Holmes et al., 1993"	778640	"LPSN"	2	"113894007"
-"B_NESSR_WEVR"	"Neisseria weaveri"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"weaveri"	""	"species"	"Holmes et al., 1993"	789964	"LPSN"	2	"113894007"
 "B_NESSR_WEIX"	"Neisseria weixii"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"weixii"	""	"species"	"Zhang et al., 2019"	5270	"LPSN"	2	"character(0)"
 "B_NESSR_ZLPH"	"Neisseria zalophi"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"zalophi"	""	"species"	"Volokhov et al., 2018"	797869	"LPSN"	2	"character(0)"
 "B_NESSR_ZDGM"	"Neisseria zoodegmatis"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Neisseriales"	"Neisseriaceae"	"Neisseria"	"zoodegmatis"	""	"species"	"Vandamme et al., 2006"	785315	"LPSN"	2	"449121005"
@@ -43144,7 +43122,6 @@
 "B_NVHRB_HUMI"	"Noviherbaspirillum humi"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"humi"	""	"species"	"Sundararaman et al., 2017"	795132	"LPSN"	2	"character(0)"
 "B_NVHRB_MLTH"	"Noviherbaspirillum malthae"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"malthae"	""	"species"	"Lin et al., 2013"	791255	"LPSN"	2	"character(0)"
 "B_NVHRB_MSSL"	"Noviherbaspirillum massiliense"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"massiliense"	""	"species"	"Chaudhary et al., 2017"	7160	"LPSN"	2	"character(0)"
-"B_NVHRB_MSSL"	"Noviherbaspirillum massiliense"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"massiliense"	""	"species"	"Chaudhary et al., 2017"	795435	"LPSN"	2	"character(0)"
 "B_NVHRB_PSYC"	"Noviherbaspirillum psychrotolerans"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"psychrotolerans"	""	"species"	"Lin et al., 2013"	791259	"LPSN"	2	"character(0)"
 "B_NVHRB_SOLI"	"Noviherbaspirillum soli"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"soli"	""	"species"	"Lin et al., 2013"	791256	"LPSN"	2	"character(0)"
 "B_NVHRB_SWNN"	"Noviherbaspirillum suwonense"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Oxalobacteraceae"	"Noviherbaspirillum"	"suwonense"	""	"species"	"Kim et al., 2014"	791816	"LPSN"	2	"character(0)"
@@ -46086,7 +46063,6 @@
 "C_PRKRN_WTZL"	"Parakeronopsis wetzeli"	"Chromista"	"Ciliophora"	"Hypotrichea"	"Stichotrichida"	"Keronidae"	"Parakeronopsis"	"wetzeli"	""	"species"	"Shi, 1999"		"CoL"	3	"character(0)"
 "B_PRLCT"	"Paralactobacillus"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Paralactobacillus"	""	""	"genus"	"Leisner et al., 2020"	516258	"LPSN"	2	"431579000"
 "B_PRLCT_SLNG"	"Paralactobacillus selangorensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Paralactobacillus"	"selangorensis"	""	"species"	"Leisner et al., 2000"	9452	"LPSN"	2	"433290004"
-"B_PRLCT_SLNG"	"Paralactobacillus selangorensis"	"Bacteria"	"Firmicutes"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Paralactobacillus"	"selangorensis"	""	"species"	"Leisner et al., 2000"	779168	"LPSN"	2	"433290004"
 "C_PRLGN"	"Paralagenidium"	"Chromista"	"Oomycota"	"Peronosporea"	"Peronosporales"	"Pythiaceae"	"Paralagenidium"	""	""	"genus"	""		"CoL"	3	"character(0)"
 "C_PRLGN_KRLN"	"Paralagenidium karlingii"	"Chromista"	"Oomycota"	"Peronosporea"	"Peronosporales"	"Pythiaceae"	"Paralagenidium"	"karlingii"	""	"species"	"Grooters et al., 2013"		"CoL"	3	"character(0)"
 "B_PRLCL"	"Paralcaligenes"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Alcaligenaceae"	"Paralcaligenes"	""	""	"genus"	""	518111	"LPSN"	2	"character(0)"
@@ -49657,7 +49633,6 @@
 "B_PHTBC_HLTL"	"Photobacterium halotolerans"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"halotolerans"	""	"species"	"Rivas et al., 2006"	779531	"LPSN"	1	"character(0)"
 "B_PHTBC_ILPS"	"Photobacterium iliopiscarium"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"iliopiscarium"	""	"species"	"Urakawa et al., 1999"	779532	"LPSN"	1	"427632007"
 "B_PHTBC_INDC"	"Photobacterium indicum"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"indicum"	""	"species"	"Ivanova et al., 2004"	7152	"LPSN"	1	"432889009"
-"B_PHTBC_INDC"	"Photobacterium indicum"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"indicum"	""	"species"	"Ivanova et al., 2004"	779533	"LPSN"	1	"432889009"
 "B_PHTBC_JEAN"	"Photobacterium jeanii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"jeanii"	""	"species"	"Chimetto et al., 2010"	788966	"LPSN"	1	"character(0)"
 "B_PHTBC_KSHT"	"Photobacterium kishitanii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"kishitanii"	""	"species"	"Ast et al., 2007"	786711	"LPSN"	1	"character(0)"
 "B_PHTBC_LGNT"	"Photobacterium leiognathi"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Photobacterium"	"leiognathi"	""	"species"	"Boisvert et al., 1967"	784624	"LPSN"	1	"115052008"
@@ -49703,7 +49678,6 @@
 "B_PHTRH_LMND_LMND"	"Photorhabdus laumondii laumondii"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"laumondii"	"laumondii"	"subsp."	"Machado et al., 2018"	798517	"LPSN"	1	"character(0)"
 "B_PHTRH_LMNS"	"Photorhabdus luminescens"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"luminescens"	""	"species"	"Boemare et al., 1999"	779539	"LPSN"	1	"115023005"
 "B_PHTRH_LMNS_LMNS"	"Photorhabdus luminescens luminescens"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"luminescens"	"luminescens"	"subsp."	"Fischer-Le Saux et al., 1999"	13667	"LPSN"	1	"432228005"
-"B_PHTRH_LMNS_LMNS"	"Photorhabdus luminescens luminescens"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"luminescens"	"luminescens"	"subsp."	"Fischer-Le Saux et al., 1999"	779543	"LPSN"	1	"432228005"
 "B_PHTRH_LMNS_MXCN"	"Photorhabdus luminescens mexicana"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"luminescens"	"mexicana"	"species"	"Machado et al., 2019"	800147	"LPSN"	1	"character(0)"
 "B_PHTRH_NMNN"	"Photorhabdus namnaonensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"namnaonensis"	""	"species"	"Machado et al., 2018"	798789	"LPSN"	1	"character(0)"
 "B_PHTRH_NNPT"	"Photorhabdus noenieputensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Enterobacterales"	"Morganellaceae"	"Photorhabdus"	"noenieputensis"	""	"species"	"Machado et al., 2018"	798693	"LPSN"	1	"character(0)"
@@ -53778,7 +53752,6 @@
 "C_PPHNA_TRTS"	"Pseudopolymorphina tortuosa"	"Chromista"	"Foraminifera"	"(unknown class)"	"Lagenida"	"Polymorphinidae"	"Pseudopolymorphina"	"tortuosa"	""	"species"	"Vella, 1957"		"CoL"	3	"character(0)"
 "C_PPHNA_VART"	"Pseudopolymorphina variata"	"Chromista"	"Foraminifera"	"(unknown class)"	"Lagenida"	"Polymorphinidae"	"Pseudopolymorphina"	"variata"	""	"species"	"Jones et al., 1866"		"CoL"	3	"character(0)"
 "C_PPHNA_VNKL"	"Pseudopolymorphina vonkleinsmidi"	"Chromista"	"Foraminifera"	"(unknown class)"	"Lagenida"	"Polymorphinidae"	"Pseudopolymorphina"	"vonkleinsmidi"	""	"species"	"McCulloch, 1977"		"CoL"	3	"character(0)"
-"B_PSDPN"	"Pseudopontixanthobacter"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Erythrobacteraceae"	"Pseudopontixanthobacter"	""	""	"genus"	"Sun et al., 2020"	14527	"LPSN"	2	"character(0)"
 "B_PSDPN"	"Pseudopontixanthobacter"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Erythrobacteraceae"	"Pseudopontixanthobacter"	""	""	"genus"	"Sun et al., 2020"	2893	"LPSN"	2	"character(0)"
 "B_PSDPN_CNFL"	"Pseudopontixanthobacter confluentis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Erythrobacteraceae"	"Pseudopontixanthobacter"	"confluentis"	""	"species"	"Liu et al., 2021"	3158	"LPSN"	2	"character(0)"
 "B_PSDPN_SDMN"	"Pseudopontixanthobacter sediminis"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Sphingomonadales"	"Erythrobacteraceae"	"Pseudopontixanthobacter"	"sediminis"	""	"species"	"Liu et al., 2021"	3209	"LPSN"	2	"character(0)"
@@ -54331,7 +54304,6 @@
 "B_[ORD]_PNCCCCLS"	"Puniceicoccales"	"Bacteria"	"Verrucomicrobia"	"Opitutae"	"Puniceicoccales"	"(unknown family)"	""	""	""	"order"	""		"CoL"	2	"character(0)"
 "B_PNCCC"	"Puniceicoccus"	"Bacteria"	"Verrucomicrobia"	"Opitutae"	"Puniceicoccales"	"Puniceicoccaceae"	"Puniceicoccus"	""	""	"genus"	""	517529	"LPSN"	3	"character(0)"
 "B_PNCCC_VRMC"	"Puniceicoccus vermicola"	"Bacteria"	"Verrucomicrobia"	"Opitutae"	"Puniceicoccales"	"Puniceicoccaceae"	"Puniceicoccus"	"vermicola"	""	"species"	"Choo et al., 2007"	786065	"LPSN"	3	"character(0)"
-"B_PSLLM"	"Pusillimonas"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Alcaligenaceae"	"Pusillimonas"	""	""	"genus"	""	516438	"LPSN"	2	"character(0)"
 "B_PSLLM"	"Pusillimonas"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Alcaligenaceae"	"Pusillimonas"	""	""	"genus"	""	3599	"LPSN"	2	"character(0)"
 "B_PSLLM_CAEN"	"Pusillimonas caeni"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Alcaligenaceae"	"Pusillimonas"	"caeni"	""	"species"	"Jin et al., 2017"	795134	"LPSN"	2	"character(0)"
 "B_PSLLM_GNSN"	"Pusillimonas ginsengisoli"	"Bacteria"	"Proteobacteria"	"Betaproteobacteria"	"Burkholderiales"	"Alcaligenaceae"	"Pusillimonas"	"ginsengisoli"	""	"species"	"Srinivasan et al., 2010"	788686	"LPSN"	2	"character(0)"
@@ -57962,7 +57934,6 @@
 "B_SLNVB_SMNS"	"Salinivibrio siamensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Salinivibrio"	"siamensis"	""	"species"	"Chamroensaksri et al., 2009"	787805	"LPSN"	1	"character(0)"
 "B_SLNVB_SCMP"	"Salinivibrio socompensis"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Vibrionales"	"Vibrionaceae"	"Salinivibrio"	"socompensis"	""	"species"	"Galisteo et al., 2020"	5551	"LPSN"	1	"character(0)"
 "B_SLNVR"	"Salinivirga"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Salinivirgaceae"	"Salinivirga"	""	""	"genus"		89	"LPSN"	3	"character(0)"
-"B_SLNVR"	"Salinivirga"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Salinivirgaceae"	"Salinivirga"	""	""	"genus"		519128	"LPSN"	3	"character(0)"
 "B_SLNVR_CYNB"	"Salinivirga cyanobacteriivorans"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Salinivirgaceae"	"Salinivirga"	"cyanobacteriivorans"	""	"species"	"Ben Hania et al., 2017"	795083	"LPSN"	3	"character(0)"
 "B_[FAM]_SALNVRGC"	"Salinivirgaceae"	"Bacteria"	"Bacteroidetes"	"Bacteroidia"	"Bacteroidales"	"Salinivirgaceae"	""	""	""	"family"			"CoL"	2	"character(0)"
 "B_SLNVM"	"Salinovum"	"Bacteria"	"Proteobacteria"	"Alphaproteobacteria"	"Rhodobacterales"	"Rhodobacteraceae"	"Salinovum"	""	""	"genus"		519197	"LPSN"	2	"character(0)"
@@ -60163,7 +60134,6 @@
 "B_SPHNGB_CIBI"	"Sphingobacterium cibi"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"cibi"	""	"species"	"Lai et al., 2016"	794899	"LPSN"	3	"character(0)"
 "B_SPHNGB_CLDN"	"Sphingobacterium cladoniae"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"cladoniae"	""	"species"	"Lee et al., 2013"	790546	"LPSN"	3	"705164003"
 "B_SPHNGB_CMPS"	"Sphingobacterium composti"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"composti"	""	"species"	"Ten et al., 2007"	785810	"LPSN"	3	"character(0)"
-"B_SPHNGB_CMPS"	"Sphingobacterium composti"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"composti"	""	"species"	"Ten et al., 2007"	786529	"LPSN"	3	"character(0)"
 "B_SPHNGB_CRTC"	"Sphingobacterium corticibacter"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"corticibacter"	""	"species"	"Li et al., 2019"	5212	"LPSN"	3	"character(0)"
 "B_SPHNGB_CTRM"	"Sphingobacterium corticibacterium"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"corticibacterium"	""	"species"	"Li et al., 2020"	14684	"LPSN"	3	"character(0)"
 "B_SPHNGB_CRTC1"	"Sphingobacterium corticis"	"Bacteria"	"Bacteroidetes"	"Sphingobacteriia"	"Sphingobacteriales"	"Sphingobacteriaceae"	"Sphingobacterium"	"corticis"	""	"species"	"Li et al., 2017"	796053	"LPSN"	3	"character(0)"
@@ -70355,7 +70325,6 @@
 "B_XNTHM_PRFR"	"Xanthomonas perforans"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"perforans"	""	"species"	"Jones et al., 2006"	785205	"LPSN"	1	"6131000146108"
 "B_XNTHM_PHSL"	"Xanthomonas phaseoli"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"phaseoli"	""	"species"	"Gabriel et al., 1989"	785206	"LPSN"	1	"440323006"
 "B_XNTHM_PISI"	"Xanthomonas pisi"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"pisi"	""	"species"	"Vauterin et al., 1995"	785207	"LPSN"	1	"439621006"
-"B_XNTHM_POPL"	"Xanthomonas populi"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"populi"	""	"species"	"Ride et al., 1992"	785208	"LPSN"	1	"439622004"
 "B_XNTHM_POPL"	"Xanthomonas populi"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"populi"	""	"species"	"Ride et al., 1992"	7159	"LPSN"	1	"439622004"
 "B_XNTHM_PRNC"	"Xanthomonas prunicola"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"prunicola"	""	"species"	"Lopez et al., 2018"	797769	"LPSN"	1	"character(0)"
 "B_XNTHM_SCCH"	"Xanthomonas sacchari"	"Bacteria"	"Proteobacteria"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Xanthomonas"	"sacchari"	""	"species"	"Vauterin et al., 1995"	786750	"LPSN"	1	"character(0)"

data-raw/mo.md5

@@ -1 +1 @@
-dbe572abad4a2dc85db8cb146b74beb9
+638a06636d8b547c2cb9d1ec243ecb7e

data-raw/reproduction_of_microorganisms_update.R

@@ -365,7 +365,9 @@ MOs <- MOs %>%
 records_ids <- taxonomy %>%
   mutate(across(1:3, function(x) { x[is.na(x)] <- ""; x}),
          fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet))) %>%
-  transmute(fullname, species_id = as.numeric(record_no))
+  transmute(fullname, species_id = as.numeric(record_no)) %>% 
+  arrange(fullname, species_id) %>% 
+  distinct(fullname, .keep_all = TRUE)
 message("Adding ", sum(records_ids$fullname %in% microorganisms$fullname), " LPSN record IDs")
 MOs <- MOs %>%
   select(-species_id) %>% 

docs/articles/datasets.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
       </span>
     </div>
 
@@ -207,7 +207,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
 <p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 November 2021 09:21:53 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 29 November 2021 10:22:24 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds">R file</a> (1.3 MB)<br>
@@ -220,7 +220,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (16.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (27.6 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (27.5 MB)</li>
 </ul>
 <p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
 <div id="source" class="section level3">

docs/news/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
       </span>
     </div>
 
@@ -232,9 +232,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719055" class="section level1">
+    <div id="amr-1719056" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9055">
+<h1 class="page-header" data-toc-text="1.7.1.9056">
-<a href="#amr-1719055" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9055</h1>
+<a href="#amr-1719056" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9056</h1>
 <div id="last-updated-29-november-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-29-november-2021" class="anchor"></a><small>Last updated: 29 November 2021</small>
@@ -325,6 +325,8 @@
 <li>The <code><a href="../reference/proportion.html">proportion_df()</a></code>, <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/proportion.html">rsi_df()</a></code> functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages</li>
 <li>The <code><a href="../reference/mdro.html">mdro()</a></code> function now returns <code>NA</code> for all rows that have no test results</li>
 <li>The <code>species_id</code> column in the <code>microorganisms</code> data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and <code><a href="../reference/mo_property.html">mo_url()</a></code> has been updated to reflect this change.</li>
+<li>Fixed a small bug in the functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code>
+</li>
 </ul>
 </div>
 <div id="other" class="section level3">

docs/reference/get_episode.html

@@ -58,8 +58,6 @@
 
 
 
-
-
 <!-- mathjax -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -71,15 +69,9 @@
 
 
 
-  
-
-  
-
   </head>
 
   <body data-spy="scroll" data-target="#toc">
-    
-
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -93,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
       </span>
     </div>
 
@@ -238,7 +230,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Determine (New) Episodes for Patients</h1>
-    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/episode.R'><code>R/episode.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/episode.R'><code>R/episode.R</code></a></small>
     <div class="hidden name"><code>get_episode.Rd</code></div>
     </div>
 
@@ -246,16 +238,16 @@
     <p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode.</p>
     </div>
 
-    <div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
+    <pre class="usage"><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
 
-<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
+<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>x</th>
-      <td><p>vector of dates (class <code>Date</code> or <code>POSIXt</code>)</p></td>
+      <td><p>vector of dates (class <code>Date</code> or <code>POSIXt</code>), will be sorted internally to determine episodes</p></td>
     </tr>
     <tr>
       <th>episode_days</th>
@@ -297,7 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
+    <pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
 <span class='co'># See ?example_isolates.</span>
 
 <span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span>    <span class='co'># indices</span>
@@ -357,7 +349,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>flag_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>
 <span class='op'>}</span>
 <span class='co'># }</span>
-</code></pre></div>
+</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -369,11 +361,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
       <footer>
       <div class="copyright">
-  <p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">
-  <p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
@@ -382,8 +374,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
   
 
 
-  
-
   </body>
 </html>
 

docs/reference/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
       </span>
     </div>
 
@@ -464,7 +464,7 @@
         <td>
           <p><code><a href="microorganisms.html">microorganisms</a></code> </p>
         </td>
-        <td><p>Data Set with 70,791 Microorganisms</p></td>
+        <td><p>Data Set with 70,760 Microorganisms</p></td>
       </tr><tr>
         
         <td>

docs/reference/microorganisms.html

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Data Set with 70,791 Microorganisms — microorganisms • AMR (for R)</title>
+<title>Data Set with 70,760 Microorganisms — microorganisms • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
 
-<meta property="og:title" content="Data Set with 70,791 Microorganisms — microorganisms" />
+<meta property="og:title" content="Data Set with 70,760 Microorganisms — microorganisms" />
 <meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary_large_image" />
@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
       </span>
     </div>
 
@@ -229,7 +229,7 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Data Set with 70,791 Microorganisms</h1>
+    <h1>Data Set with 70,760 Microorganisms</h1>
     <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.Rd</code></div>
     </div>
@@ -243,7 +243,7 @@
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,791 observations and 16 variables:</p><ul>
+    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,760 observations and 16 variables:</p><ul>
 <li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>

inst/tinytest/test-episode.R

@@ -35,6 +35,10 @@ test_df <- rbind(
 
 expect_equal(get_episode(test_df$date, 365),
              c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
+expect_equal(get_episode(test_df$date[which(test_df$patient_id == "A")], 365),
+             c(1, 1, 2, 2, 2, 2, 3, 4))
+expect_equal(get_episode(test_df$date[which(test_df$patient_id == "B")], 365),
+             c(1, 2, 2, 2, 3))
 
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),

inst/tinytest/test-mdro.R

@@ -40,7 +40,7 @@ expect_identical(class(outcome), c("ordered", "factor"))
 
 # example_isolates should have these finding using Dutch guidelines
 expect_equal(as.double(table(outcome)),
-             c(1970, 24, 6)) # 1970 neg, 24 unconfirmed, 6 pos
+             c(1954, 24, 6)) # 1954 neg, 24 unconfirmed, 6 pos, rest is NA
 
 expect_equal(brmo(example_isolates, info = FALSE),
              mdro(example_isolates, guideline = "BRMO", info = FALSE))

man/get_episode.Rd

@@ -10,7 +10,7 @@ get_episode(x, episode_days, ...)
 is_new_episode(x, episode_days, ...)
 }
 \arguments{
-\item{x}{vector of dates (class \code{Date} or \code{POSIXt})}
+\item{x}{vector of dates (class \code{Date} or \code{POSIXt}), will be sorted internally to determine episodes}
 
 \item{episode_days}{required episode length in days, can also be less than a day or \code{Inf}, see \emph{Details}}
 

man/microorganisms.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data Set with 70,791 Microorganisms}
+\title{Data Set with 70,760 Microorganisms}
 \format{
-A \link{data.frame} with 70,791 observations and 16 variables:
+A \link{data.frame} with 70,760 observations and 16 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}