diff --git a/DESCRIPTION b/DESCRIPTION index 94c3bf4f..80a90303 100644 --- a/DESCRIPTION +++ b/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) diff --git a/NEWS.md b/NEWS.md index 69bcbc17..20a10107 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9055 +# `AMR` 1.7.1.9056 ## Last updated: 29 November 2021 ### 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. diff --git a/R/episode.R b/R/episode.R index 150d4e62..90bd8cf3 100644 --- a/R/episode.R +++ b/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)] } diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 5fd244ae..de431cce 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/microorganisms.dta b/data-raw/microorganisms.dta index 5557752a..4496f348 100644 Binary files a/data-raw/microorganisms.dta and b/data-raw/microorganisms.dta differ diff --git a/data-raw/microorganisms.rds b/data-raw/microorganisms.rds index b56f3906..e1e4dd8f 100644 Binary files a/data-raw/microorganisms.rds and b/data-raw/microorganisms.rds differ diff --git a/data-raw/microorganisms.sas b/data-raw/microorganisms.sas index d143a5cc..2eb2d840 100644 Binary files a/data-raw/microorganisms.sas and b/data-raw/microorganisms.sas differ diff --git a/data-raw/microorganisms.sav b/data-raw/microorganisms.sav index 69e1c96f..dfb50663 100644 Binary files a/data-raw/microorganisms.sav and b/data-raw/microorganisms.sav differ diff --git a/data-raw/microorganisms.txt b/data-raw/microorganisms.txt index bf3436dc..0dfd6d7e 100644 --- a/data-raw/microorganisms.txt +++ b/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)" diff --git a/data-raw/mo.md5 b/data-raw/mo.md5 index 49442ae8..81fec19e 100644 --- a/data-raw/mo.md5 +++ b/data-raw/mo.md5 @@ -1 +1 @@ -dbe572abad4a2dc85db8cb146b74beb9 +638a06636d8b547c2cb9d1ec243ecb7e diff --git a/data-raw/reproduction_of_microorganisms_update.R b/data-raw/reproduction_of_microorganisms_update.R index c62cd163..f08c4111 100644 --- a/data-raw/reproduction_of_microorganisms_update.R +++ b/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) %>% diff --git a/data/microorganisms.rda b/data/microorganisms.rda index 01b577da..7427ee7d 100644 Binary files a/data/microorganisms.rda and b/data/microorganisms.rda differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index d66a2e5e..60119012 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9055 + 1.7.1.9056 @@ -207,7 +207,7 @@ If you are reading this page from within R, please Microorganisms (currently accepted names)

A data set with 70,760 rows and 16 columns, containing the following column names:
mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence and snomed.

This data set is in R available as microorganisms, after you load the AMR package.

-

It was last updated on 29 November 2021 09:21:53 UTC. Find more info about the structure of this data set here.

+

It was last updated on 29 November 2021 10:22:24 UTC. Find more info about the structure of this data set here.

Direct download links:

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. Advice? Use R instead.

diff --git a/docs/news/index.html b/docs/news/index.html index b1a5bb16..387590b7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 1.7.1.9055 + 1.7.1.9056
@@ -232,9 +232,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9055

+
+

+ Unreleased AMR 1.7.1.9056

Last updated: 29 November 2021 @@ -325,6 +325,8 @@
  • 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() +

    • diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html index c1123078..690e139e 100644 --- a/docs/reference/get_episode.html +++ b/docs/reference/get_episode.html @@ -58,8 +58,6 @@ - - @@ -71,15 +69,9 @@ - - - - - -
    @@ -238,7 +230,7 @@

    Determine (New) Episodes for Patients

    - Source: R/episode.R + Source: R/episode.R
    @@ -246,16 +238,16 @@

    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.

    - 
    get_episode(x, episode_days, ...)
+    
    get_episode(x, episode_days, ...)
 
-is_new_episode(x, episode_days, ...)
    +is_new_episode(x, episode_days, ...)

    Arguments

    - + @@ -297,7 +289,7 @@ The lifecycle of this function is stable

    first_isolate()

    Examples

    - 
    # `example_isolates` is a data set available in the AMR package.
+    
    # `example_isolates` is a data set available in the AMR package.
 # See ?example_isolates.
 
 get_episode(example_isolates$date, episode_days = 60)    # indices
@@ -357,7 +349,7 @@ The lifecycle of this function is stablemutate(flag_episode = is_new_episode(date, 365))
 }
 # }
-
    + @@ -464,7 +464,7 @@     - +
    x

    vector of dates (class Date or POSIXt)

    vector of dates (class Date or POSIXt), will be sorted internally to determine episodes
    episode_days

    microorganisms

    Data Set with 70,791 Microorganisms

    Data Set with 70,760 Microorganisms
    diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index a31c5652..5daa82d6 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -6,7 +6,7 @@ -Data Set with 70,791 Microorganisms — microorganisms • AMR (for R) +Data Set with 70,760 Microorganisms — microorganisms • AMR (for R) @@ -48,7 +48,7 @@ - + @@ -85,7 +85,7 @@ AMR (for R) - 1.7.1.9055 + 1.7.1.9056 @@ -229,7 +229,7 @@
    -

    Data Set with 70,791 Microorganisms

    +

    Data Set with 70,760 Microorganisms

    Source: R/data.R
    @@ -243,7 +243,7 @@

    Format

    -

    A data.frame with 70,791 observations and 16 variables:

      +

      A data.frame with 70,760 observations and 16 variables:

      • mo
        ID of microorganism as used by this package

      • fullname
        Full name, like "Escherichia coli"

      • kingdom, phylum, class, order, family, genus, species, subspecies
        Taxonomic rank of the microorganism

        • diff --git a/inst/tinytest/test-episode.R b/inst/tinytest/test-episode.R index 89932ffd..948d06d9 100644 --- a/inst/tinytest/test-episode.R +++ b/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), diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R index 22c717b2..057975c4 100755 --- a/inst/tinytest/test-mdro.R +++ b/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)) diff --git a/man/get_episode.Rd b/man/get_episode.Rd index a3f7b581..1e0bc1ac 100644 --- a/man/get_episode.Rd +++ b/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}} diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 7c022906..9afb6f38 100755 --- a/man/microorganisms.Rd +++ b/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"}