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(v1.8.1.9012) update prevalence of some genera

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dr. M.S. (Matthijs) Berends 2022-06-03 13:28:55 +02:00
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DESCRIPTION
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Package: AMR
Version: 1.8.1.9011
Version: 1.8.1.9012
Date: 2022-06-03
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# `AMR` 1.8.1.9011
# `AMR` 1.8.1.9012
## <small>Last updated: 3 June 2022</small>
### New

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R/atc_online.R
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#'
#' - `"g"` = gram
#' - `"mg"` = milligram
#' - `"mcg"`` = microgram
#' - `"mcg"` = microgram
#' - `"U"` = unit
#' - `"TU"` = thousand units
#' - `"MU"` = million units

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R/custom_eucast_rules.R
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#'
#' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
#' @inheritSection lifecycle Stable Lifecycle
#' @param ... rules in formula notation, see *Examples*
#' @param ... rules in [formula][`~`()] notation, see *Examples*
#' @details
#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
#'
@ -75,7 +75,7 @@
#'
#' ### Using taxonomic properties in rules
#'
#' There is one exception in variables used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
#' There is one exception in variables used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), quote = "\u0096", sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
#'
#' ```
#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
@ -91,7 +91,7 @@
#'
#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
#'
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\u0096", tolower(gsub("^AB_", "", x)), "\u0096\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
#' @returns A [list] containing the custom rules
#' @inheritSection AMR Read more on Our Website!
#' @export

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R/resistance_predict.R
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#' @param year_max highest year to use in the prediction model, defaults to 10 years after today
#' @param year_every unit of sequence between lowest year found in the data and `year_max`
#' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)`, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
#' @param I_as_S a [logical] to indicate whether values `"I"` should be treated as `"S"` (will otherwise be treated as `"R"`). The default, `TRUE`, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section *Interpretation of S, I and R* below.
#' @param preserve_measurements a [logical] to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be `NA`.
#' @param info a [logical] to indicate whether textual analysis should be printed with the name and [summary()] of the statistical model.

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data-raw/microorganisms.old.md5
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data-raw/microorganisms.old.txt
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@ -278,9 +278,9 @@
"Adelosina duthiersi" "Quinqueloculina duthiersi" "Schlumberger, 1886" 3
"Adelosina linneiana" "Pseudotriloculina linneiana" "DOrbigny, 1839" 3
"Aecidium ipomoeae-panduratae" "Albugo ipomoeae-panduratae" "Schwein, 1822" 3
"Aedimorphus alboannulatus" "Aedes alboannulatus" "Theobald, 1905" 3
"Aedimorphus albotaeniatus" "Aedes albotaeniatus" "Theobald, 1903" 3
"Aedimorphus australis" "Aedes australis" "Taylor, 1914" 3
"Aedimorphus alboannulatus" "Aedes alboannulatus" "Theobald, 1905" 2
"Aedimorphus albotaeniatus" "Aedes albotaeniatus" "Theobald, 1903" 2
"Aedimorphus australis" "Aedes australis" "Taylor, 1914" 2
"Aegyria angustata" "Dysteria angustata" "Claparede et al., 1859" 3
"Aegyria astyla" "Dysteria astyla" "Maskell, 1887" 3
"Aegyria distyla" "Dysteria distyla" "Maskell, 1887" 3
@ -880,7 +880,7 @@
"Astacolus subaculeata" "Vaginulinopsis subaculeata" "Cushman, 1923" 3
"Astacolus sublegumen" "Vaginulinopsis sublegumen" "Parr, 1950" 3
"Asterellina pulchella" "Eoeponidella pulchella" "Parker, 1952" 3
"Asterias ocellifera" "Nectria ocellifera" "Lamarck, 1816" 3
"Asterias ocellifera" "Nectria ocellifera" "Lamarck, 1816" 2
"Asterigerinata pulchella" "Eoeponidella pulchella" "Parker, 1952" 3
"Asteromella anthemidis" "Phoma anthemidis" "Ruppr, 1958" 2
"Asteromella longissima" "Phoma longissima" "Petr" 2
@ -1324,8 +1324,8 @@
"Bacteriovorax marinus" "Halobacteriovorax marinus" "Baer et al., 2004" 2
"Bacteriovorax starrii" "Peredibacter starrii" "Baer et al., 2000" 2
"Bacteroides amylophilus" "Ruminobacter amylophilus" "Hamlin et al., 1956" 1
"Bacteroides asaccharolyticus" "Porphyromonas asaccharolytica" "Finegold et al., 1977" 3
"Bacteroides barnesiae" "Phocaeicola barnesiae" "Lan et al., 2006" 3
"Bacteroides asaccharolyticus" "Porphyromonas asaccharolytica" "Finegold et al., 1977" 2
"Bacteroides barnesiae" "Phocaeicola barnesiae" "Lan et al., 2006" 2
"Bacteroides bivius" "Prevotella bivia" "Holdeman et al., 1977" 2
"Bacteroides buccae" "Prevotella buccae" "Holdeman et al., 1982" 2
"Bacteroides buccalis" "Prevotella buccalis" "Shah et al., 1982" 2
@ -1333,32 +1333,32 @@
"Bacteroides capillus" "Prevotella buccae" "Kornman et al., 1982" 2
"Bacteroides cellulosolvens" "Pseudobacteroides cellulosolvens" "Murray et al., 1984" 2
"Bacteroides chinchillae" "Bacteroides sartorii" "Kitahara et al., 2011"
"Bacteroides chinchillae" "Phocaeicola sartorii" "Kitahara et al., 2011" 3
"Bacteroides chinchillae" "Phocaeicola sartorii" "Kitahara et al., 2011" 2
"Bacteroides coagulans" "Ezakiella coagulans" "Eggerth et al., 1933" 2
"Bacteroides coprocola" "Phocaeicola coprocola" "Kitahara et al., 2005" 3
"Bacteroides coprophilus" "Phocaeicola coprophilus" "Hayashi et al., 2016" 3
"Bacteroides coprocola" "Phocaeicola coprocola" "Kitahara et al., 2005" 2
"Bacteroides coprophilus" "Phocaeicola coprophilus" "Hayashi et al., 2016" 2
"Bacteroides corporis" "Prevotella corporis" "Johnson et al., 1983" 2
"Bacteroides denticola" "Prevotella denticola" "Shah et al., 1982" 2
"Bacteroides disiens" "Prevotella disiens" "Holdeman et al., 1977" 2
"Bacteroides distasonis" "Parabacteroides distasonis" "Eggerth et al., 1933" 3
"Bacteroides dorei" "Phocaeicola dorei" "Bakir et al., 2016" 3
"Bacteroides endodontalis" "Porphyromonas endodontalis" "Van Steenbergen et al., 1984" 3
"Bacteroides distasonis" "Parabacteroides distasonis" "Eggerth et al., 1933" 2
"Bacteroides dorei" "Phocaeicola dorei" "Bakir et al., 2016" 2
"Bacteroides endodontalis" "Porphyromonas endodontalis" "Van Steenbergen et al., 1984" 2
"Bacteroides forsythus" "Tannerella forsythia" "Tanner et al., 1986" 3
"Bacteroides furcosus" "Anaerorhabdus furcosa" "Hauduroy et al., 1937" 2
"Bacteroides gingivalis" "Porphyromonas gingivalis" "Coykendall et al., 1980" 3
"Bacteroides goldsteinii" "Parabacteroides goldsteinii" "Song et al., 2006" 3
"Bacteroides gingivalis" "Porphyromonas gingivalis" "Coykendall et al., 1980" 2
"Bacteroides goldsteinii" "Parabacteroides goldsteinii" "Song et al., 2006" 2
"Bacteroides gracilis" "Campylobacter gracilis" "Tanner et al., 1981" 2
"Bacteroides heparinolyticus" "Prevotella heparinolytica" "Okuda et al., 1985" 2
"Bacteroides hypermegas" "Megamonas hypermegale" "Harrison et al., 1963" 2
"Bacteroides intermedius" "Prevotella intermedia" "Johnson et al., 1983" 2
"Bacteroides levii" "Porphyromonas levii" "Johnson et al., 1983" 3
"Bacteroides levii" "Porphyromonas levii" "Johnson et al., 1983" 2
"Bacteroides loescheii" "Prevotella loescheii" "Holdeman et al., 1982" 2
"Bacteroides macacae" "Porphyromonas macacae" "Coykendall et al., 1980" 3
"Bacteroides massiliensis" "Phocaeicola massiliensis" "Fenner et al., 2016" 3
"Bacteroides macacae" "Porphyromonas macacae" "Coykendall et al., 1980" 2
"Bacteroides massiliensis" "Phocaeicola massiliensis" "Fenner et al., 2016" 2
"Bacteroides melaninogenicus" "Prevotella melaninogenica" "Roy et al., 1982" 2
"Bacteroides melaninogenicus intermedius" "Prevotella intermedia" "Holdeman et al., 1970" 2
"Bacteroides melaninogenicus macacae" "Porphyromonas macacae" "Slots et al., 1980" 3
"Bacteroides merdae" "Parabacteroides merdae" "Johnson et al., 1986" 3
"Bacteroides melaninogenicus macacae" "Porphyromonas macacae" "Slots et al., 1980" 2
"Bacteroides merdae" "Parabacteroides merdae" "Johnson et al., 1986" 2
"Bacteroides microfusus" "Rikenella microfusus" "Kaneuchi et al., 1978" 3
"Bacteroides multiacidus" "Mitsuokella multacida" "Mitsuoka et al., 1974" 2
"Bacteroides nodosus" "Dichelobacter nodosus" "Mraz, 1963" 1
@ -1366,19 +1366,19 @@
"Bacteroides oralis" "Prevotella oralis" "Loesche et al., 1964" 2
"Bacteroides oris" "Prevotella oris" "Holdeman et al., 1982" 2
"Bacteroides oulorum" "Prevotella oulorum" "Shah et al., 1985" 2
"Bacteroides paurosaccharolyticus" "Phocaeicola paurosaccharolyticus" "Ueki et al., 2011" 3
"Bacteroides paurosaccharolyticus" "Phocaeicola paurosaccharolyticus" "Ueki et al., 2011" 2
"Bacteroides pentosaceus" "Prevotella buccae" "Shah et al., 1982" 2
"Bacteroides plebeius" "Phocaeicola plebeius" "Kitahara et al., 2005" 3
"Bacteroides plebeius" "Phocaeicola plebeius" "Kitahara et al., 2005" 2
"Bacteroides pneumosintes" "Dialister pneumosintes" "Holdeman et al., 1970" 2
"Bacteroides praeacutus" "Tissierella praeacuta" "Holdeman et al., 1970" 2
"Bacteroides putredinis" "Alistipes putredinis" "Kelly, 1957" 3
"Bacteroides putredinis" "Alistipes putredinis" "Kelly, 1957" 2
"Bacteroides ruminicola" "Prevotella ruminicola" "Bryant et al., 1958" 2
"Bacteroides ruminicola brevis" "Prevotella brevis" "Bryant et al., 1958" 2
"Bacteroides salanitronis" "Phocaeicola salanitronis" "Lan et al., 2006" 3
"Bacteroides salivosus" "Porphyromonas macacae" "Love et al., 1987" 3
"Bacteroides salanitronis" "Phocaeicola salanitronis" "Lan et al., 2006" 2
"Bacteroides salivosus" "Porphyromonas macacae" "Love et al., 1987" 2
"Bacteroides salyersae" "Bacteroides salyersiae" "Song et al., 2005" 2
"Bacteroides sartorii" "Phocaeicola sartorii" "Clavel et al., 2012" 3
"Bacteroides splanchnicus" "Odoribacter splanchnicus" "Werner et al., 1975" 3
"Bacteroides sartorii" "Phocaeicola sartorii" "Clavel et al., 2012" 2
"Bacteroides splanchnicus" "Odoribacter splanchnicus" "Werner et al., 1975" 2
"Bacteroides succinogenes" "Fibrobacter succinogenes" "Hungate, 1950" 3
"Bacteroides suis" "Bacteroides pyogenes" "Benno et al., 1983" 2
"Bacteroides tectum" "Bacteroides pyogenes" "Love et al., 2019" 2
@ -1386,7 +1386,7 @@
"Bacteroides termitidis" "Sebaldella termitidis" "Holdeman et al., 1970" 3
"Bacteroides ureolyticus" "Campylobacter ureolyticus" "Jackson et al., 1978" 2
"Bacteroides veroralis" "Prevotella veroralis" "Watabe et al., 1983" 2
"Bacteroides vulgatus" "Phocaeicola vulgatus" "Hahnke et al., 2016" 3
"Bacteroides vulgatus" "Phocaeicola vulgatus" "Hahnke et al., 2016" 2
"Bacteroides xylanolyticus" "Hungatella xylanolytica" "Scholten-Koerselman et al., 1988" 2
"Bacteroides zoogleoformans" "Prevotella zoogleoformans" "Cato et al., 1982"
"Bacteroides zoogleoformans" "Capsularis zoogleoformans" "Cato et al., 1982" 3
@ -1650,27 +1650,27 @@
"Bolivinita subangularis" "Saidovina subangularis" "Brady, 1881" 3
"Bolivinita subangularis lineata" "Saidovina subangularis lineata" "Cushman, 1933" 3
"Borelis (Fasciolites) pygmaea" "Neoalveolina pygmaea" "Hanzawa, 1930" 3
"Borrelia baltazardi" "Borrelia baltazardii" "Karimi et al., 1983" 3
"Borrelia bavariensis" "Borrelia garinii bavariensis" "Margos et al., 2020" 3
"Borrelia turdae" "Borrelia turdi" "Fukunaga et al., 1997" 3
"Borreliella" "Borrelia" "Adeolu et al., 2015" 3
"Borreliella afzelii" "Borrelia afzelii" "Adeolu et al., 2018" 3
"Borreliella americana" "Borrelia americana" "Adeolu et al., 2018" 3
"Borrelia baltazardi" "Borrelia baltazardii" "Karimi et al., 1983" 2
"Borrelia bavariensis" "Borrelia garinii bavariensis" "Margos et al., 2020" 2
"Borrelia turdae" "Borrelia turdi" "Fukunaga et al., 1997" 2
"Borreliella" "Borrelia" "Adeolu et al., 2015" 2
"Borreliella afzelii" "Borrelia afzelii" "Adeolu et al., 2018" 2
"Borreliella americana" "Borrelia americana" "Adeolu et al., 2018" 2
"Borreliella bavariensis" "Borrelia bavariensis" "Adeolu et al., 2015"
"Borreliella bavariensis" "Borrelia garinii bavariensis" "Adeolu et al., 2015" 3
"Borreliella bissettiae" "Borrelia bissettiae" "Gupta, 2020" 3
"Borreliella burgdorferi" "Borrelia burgdorferi" "Adeolu et al., 2015" 3
"Borreliella californiensis" "Borrelia californiensis" "Gupta, 2020" 3
"Borreliella carolinensis" "Borrelia carolinensis" "Adeolu et al., 2015" 3
"Borreliella garinii" "Borrelia garinii" "Adeolu et al., 2015" 3
"Borreliella japonica" "Borrelia japonica" "Adeolu et al., 2015" 3
"Borreliella kurtenbachii" "Borrelia kurtenbachii" "Adeolu et al., 2015" 3
"Borreliella lanei" "Borrelia lanei" "Gupta, 2020" 3
"Borreliella mayonii" "Borrelia mayonii" "Gupta, 2020" 3
"Borreliella sinica" "Borrelia sinica" "Adeolu et al., 2015" 3
"Borreliella spielmanii" "Borrelia spielmanii" "Adeolu et al., 2015" 3
"Borreliella valaisiana" "Borrelia valaisiana" "Adeolu et al., 2018" 3
"Borreliella yangtzensis" "Borrelia yangtzensis" "Gupta, 2020" 3
"Borreliella bavariensis" "Borrelia garinii bavariensis" "Adeolu et al., 2015" 2
"Borreliella bissettiae" "Borrelia bissettiae" "Gupta, 2020" 2
"Borreliella burgdorferi" "Borrelia burgdorferi" "Adeolu et al., 2015" 2
"Borreliella californiensis" "Borrelia californiensis" "Gupta, 2020" 2
"Borreliella carolinensis" "Borrelia carolinensis" "Adeolu et al., 2015" 2
"Borreliella garinii" "Borrelia garinii" "Adeolu et al., 2015" 2
"Borreliella japonica" "Borrelia japonica" "Adeolu et al., 2015" 2
"Borreliella kurtenbachii" "Borrelia kurtenbachii" "Adeolu et al., 2015" 2
"Borreliella lanei" "Borrelia lanei" "Gupta, 2020" 2
"Borreliella mayonii" "Borrelia mayonii" "Gupta, 2020" 2
"Borreliella sinica" "Borrelia sinica" "Adeolu et al., 2015" 2
"Borreliella spielmanii" "Borrelia spielmanii" "Adeolu et al., 2015" 2
"Borreliella valaisiana" "Borrelia valaisiana" "Adeolu et al., 2018" 2
"Borreliella yangtzensis" "Borrelia yangtzensis" "Gupta, 2020" 2
"Botryonipha aurantiaca" "Nectria aurantiaca" "Kuntze, 1891" 2
"Botryonipha flavipes" "Trichoderma flavipes" "Kuntze, 1891" 2
"Botryopyle setosa" "Amphimelissa setosa" "Cleve, 1899" 3
@ -1857,9 +1857,9 @@
"Buliminoides curta" "Seiglieina curta" "Seiglie, 1965" 3
"Buliminoides laevigata" "Fredsmithia laevigata" "Seiglie, 1964" 3
"Buliminoides milletti" "Floresina milletti" "Cushman, 1933" 3
"Buliminus mantongensis" "Giardia mantongensis" "Kobelt, 1899" 3
"Buliminus pharangensis" "Giardia pharangensis" "Dautzenberg et al., 1905" 3
"Bulimus siamensis" "Giardia siamensis" "Redfield, 1853" 3
"Buliminus mantongensis" "Giardia mantongensis" "Kobelt, 1899" 2
"Buliminus pharangensis" "Giardia pharangensis" "Dautzenberg et al., 1905" 2
"Bulimus siamensis" "Giardia siamensis" "Redfield, 1853" 2
"Bulla ovum" "Ovum ovum" "Linnaeus, 1758" 3
"Bullera aurantiaca" "Dioszegia aurantiaca" "Johri et al., 1984" 3
"Bullera begoniae" "Bulleribasidium begoniae" "Nakase et al., 2004" 3
@ -2009,7 +2009,7 @@
"Caliciopsis calicioides" "Exophiala calicioides" "Fitzp, 1920" 2
"Calidifontibacillus azotoformans" "Schinkia azotoformans" "Adiguzel et al., 2020" 2
"Calidifontibacillus oryziterrae" "Schinkia oryziterrae" "Adiguzel et al., 2020" 2
"Calliphora bicolor" "Lucilia bicolor" "Macquart, 1843" 3
"Calliphora bicolor" "Lucilia bicolor" "Macquart, 1843" 2
"Calomyxa longifila" "Minakatella longifila" "LGKrieglst, 1990" 3
"Calonectria calami" "Nectria calami" "Henn et al., 1900" 2
"Calonectria citrinoaurantia" "Nectria citrinoaurantia" "Sacc, 1883" 2
@ -2302,7 +2302,7 @@
"Cavostelium bisporum" "Echinostelium bisporum" "LSOlive et al., 1966" 3
"Celeribacter manganoxidans" "Pacificitalea manganoxidans" "Wang et al., 2015" 2
"Cellanthus biperforatus" "Elphidium biperforatus" "Whittaker et al., 1979" 3
"Cellia pretoriensis" "Anopheles pretoriensis" "Gough, 1910" 3
"Cellia pretoriensis" "Anopheles pretoriensis" "Gough, 1910" 2
"Cellulomonas cartae" "Cellulosimicrobium cellulans" "Stackebrandt et al., 1980" 2
"Cellulomonas cellulans" "Cellulosimicrobium cellulans" "Stackebrandt et al., 1988" 2
"Cellulomonas fermentans" "Actinotalea fermentans" "Bagnara et al., 1985" 2
@ -2522,11 +2522,11 @@
"Chlamydonella distyla" "Wilbertella distyla" "Jankowski, 2007" 3
"Chlamydonella polonica" "Chlamydonellopsis polonica" "Foissner et al., 1981" 3
"Chlamydonella stricta" "Wilbertiella stricta" "Deroux, 1976" 3
"Chlamydophila abortus" "Chlamydia abortus" "Everett et al., 1999" 3
"Chlamydophila felis" "Chlamydia felis" "Everett et al., 1999" 3
"Chlamydophila pecorum" "Chlamydia pecorum" "Everett et al., 1999" 3
"Chlamydophila pneumoniae" "Chlamydia pneumoniae" "Everett et al., 1999" 3
"Chlamydophila psittaci" "Chlamydia psittaci" "Everett et al., 1999" 3
"Chlamydophila abortus" "Chlamydia abortus" "Everett et al., 1999" 2
"Chlamydophila felis" "Chlamydia felis" "Everett et al., 1999" 2
"Chlamydophila pecorum" "Chlamydia pecorum" "Everett et al., 1999" 2
"Chlamydophila pneumoniae" "Chlamydia pneumoniae" "Everett et al., 1999" 2
"Chlamydophila psittaci" "Chlamydia psittaci" "Everett et al., 1999" 2
"Chlamydotomus beigelii" "Geotrichum beigelii" "Trevis, 1879" 3
"Chlamydozyma pulcherrima" "Metschnikowia pulcherrima" "Wick, 1964" 3
"Chlamydozyma reukaufii" "Metschnikowia reukaufii" "Wick, 1964" 3
@ -2599,8 +2599,8 @@
"Chrysalogonium piramidale" "Acostina piramidale" "Acosta, 1940" 3
"Chryseobacterium arothri" "Chryseobacterium hominis" "Campbell et al., 2008" 2
"Chryseobacterium greenlandense" "Chryseobacterium aquaticum greenlandense" "Loveland-Curtze et al., 2016" 2
"Chryseobacterium meningosepticum" "Elizabethkingia meningoseptica" "Vandamme et al., 1994" 3
"Chryseobacterium miricola" "Elizabethkingia miricola" "Li et al., 2004" 3
"Chryseobacterium meningosepticum" "Elizabethkingia meningoseptica" "Vandamme et al., 1994" 2
"Chryseobacterium miricola" "Elizabethkingia miricola" "Li et al., 2004" 2
"Chryseomonas" "Pseudomonas" "Holmes et al., 1987" 1
"Chryseomonas luteola" "Pseudomonas luteola" "Holmes et al., 1987" 1
"Chryseomonas polytricha" "Pseudomonas luteola" "Holmes et al., 1986" 1
@ -3331,11 +3331,11 @@
"Cucurbitaria urceolus" "Nectria urceolus" "Kuntze, 1898" 2
"Cucurbitaria uredinicola" "Nectria uredinicola" "Kuntze, 1898" 2
"Cucurbitaria verrucosa" "Nectria verrucosa" "Kuntze, 1898" 2
"Culex auratus" "Aedes auratus" "Leicester, 1908" 3
"Culex sticticus" "Aedes sticticus" "Meigen, 1838" 3
"Culex sudanensis" "Aedes sudanensis" "Theobald, 1911" 3
"Culex sylvaticus" "Aedes sylvaticus" "Meigen, 1818" 3
"Culicada annulipes" "Aedes annulipes" "Taylor, 1914" 3
"Culex auratus" "Aedes auratus" "Leicester, 1908" 2
"Culex sticticus" "Aedes sticticus" "Meigen, 1838" 2
"Culex sudanensis" "Aedes sudanensis" "Theobald, 1911" 2
"Culex sylvaticus" "Aedes sylvaticus" "Meigen, 1818" 2
"Culicada annulipes" "Aedes annulipes" "Taylor, 1914" 2
"Cuneolina angusta" "Textulariella angusta" "Cushman, 1919" 3
"Cunninghamia infundibulifera" "Choanephora infundibulifera" "Curr, 1873" 3
"Cupravidus yeoncheonense" "Cupriavidus yeoncheonensis" "Singh et al., 2015" 2
@ -3456,11 +3456,11 @@
"Cytophaga diffluens" "Persicobacter diffluens" "Reichenbach, 1989" 3
"Cytophaga fermentans" "Saccharicrinis fermentans" "Bachmann, 1955" 3
"Cytophaga flevensis" "Flavobacterium flevense" "Van der Meulen et al., 1974" 2
"Cytophaga heparina" "Pedobacter heparinus" "Christensen, 1980" 3
"Cytophaga heparina" "Pedobacter heparinus" "Christensen, 1980" 2
"Cytophaga johnsonae" "Flavobacterium johnsoniae" "Stanier, 1947" 2
"Cytophaga latercula" "Aquimarina latercula" "Lewin, 1969" 3
"Cytophaga lytica" "Cellulophaga lytica" "Lewin, 1969" 3
"Cytophaga marina" "Tenacibaculum maritimum" "Reichenbach, 1989" 3
"Cytophaga marina" "Tenacibaculum maritimum" "Reichenbach, 1989" 2
"Cytophaga marinoflava" "Leeuwenhoekiella marinoflava" "Reichenbach, 1989" 3
"Cytophaga pectinovora" "Flavobacterium pectinovorum" "Reichenbach, 1989" 2
"Cytophaga psychrophila" "Flavobacterium psychrophilum" "Reichenbach, 1989" 2
@ -3514,11 +3514,11 @@
"Defluviimonas pyrenivorans" "Acidimangrovimonas pyrenivorans" "Zhang et al., 2018" 2
"Dehalospirillum" "Sulfurospirillum" "Scholz-Muramatsu et al., 2002" 2
"Dehalospirillum multivorans" "Sulfurospirillum multivorans" "Scholz-Muramatsu et al., 2002" 2
"Deinobacter" "Deinococcus" "Oyaizu et al., 1987" 3
"Deinobacter grandis" "Deinococcus grandis" "Oyaizu et al., 1987" 3
"Deinobacter" "Deinococcus" "Oyaizu et al., 1987" 2
"Deinobacter grandis" "Deinococcus grandis" "Oyaizu et al., 1987" 2
"Deinococcus erythromyxa" "Kocuria rosea" "Brooks et al., 1981" 2
"Deinococcus mumbaiensis" "Deinococcus ficus" "Shashidhar et al., 2006" 3
"Deinococcus xibeiensis" "Deinococcus wulumuqiensis" "Wang et al., 2010" 3
"Deinococcus mumbaiensis" "Deinococcus ficus" "Shashidhar et al., 2006" 2
"Deinococcus xibeiensis" "Deinococcus wulumuqiensis" "Wang et al., 2010" 2
"Dekkeromyces aestuarii" "Kluyveromyces aestuarii" "Kock-Krat, 1982" 3
"Dekkeromyces delphensis" "Nakaseomyces delphensis" "Novak et al., 1961" 3
"Dekkeromyces dobzhanskii" "Kluyveromyces dobzhanskii" "Santa Maria et al., 1970" 3
@ -3745,7 +3745,7 @@
"Deuterammina williamsoni" "Lepidodeuterammina williamsoni" "Bronnimann et al., 1988" 3
"Devosia nitraria" "Devosia nitrariae" "Xu et al., 2018" 2
"Devosia subaequoris" "Devosia soli" "Lee, 2007" 2
"Dexiogonimus ciureanus" "Metagonimus ciureanus" "Witenberg, 1929" 3
"Dexiogonimus ciureanus" "Metagonimus ciureanus" "Witenberg, 1929" 2
"Dexiotricha centralis" "Dexiotrichides centralis" "Stokes, 1885" 3
"Diacanthocapsa brevithorax" "Theocapsomma brevithorax" "Dumitrica, 1970" 3
"Diachaeella bulbillosa" "Diachea bulbillosa" "Hohn, 1909" 3
@ -3772,11 +3772,11 @@
"Diaphorobacter polyhydroxybutyrativorans" "Diaphorobacter nitroreducens" "Qiu et al., 2015" 2
"Diatoma anceps" "Meridion anceps" "Kirchn" 3
"Diatoma hyalina" "Fragilaria hyalina" "Kutzing" 3
"Dibothriocephalus archeri" "Diphyllobothrium archeri" "Leiper et al., 1914" 3
"Dibothriocephalus hians" "Diphyllobothrium hians" "Luhe, 1899" 3
"Dibothriocephalus lashleyi" "Diphyllobothrium lashleyi" "Leiper et al., 1914" 3
"Dibothriocephalus pygoscelis" "Diphyllobothrium pygoscelis" "Rennie et al., 1912" 3
"Dibothriocephalus schistochilus" "Diphyllobothrium schistochilus" "Germanos, 1895" 3
"Dibothriocephalus archeri" "Diphyllobothrium archeri" "Leiper et al., 1914" 2
"Dibothriocephalus hians" "Diphyllobothrium hians" "Luhe, 1899" 2
"Dibothriocephalus lashleyi" "Diphyllobothrium lashleyi" "Leiper et al., 1914" 2
"Dibothriocephalus pygoscelis" "Diphyllobothrium pygoscelis" "Rennie et al., 1912" 2
"Dibothriocephalus schistochilus" "Diphyllobothrium schistochilus" "Germanos, 1895" 2
"Dicaeoma brassicae" "Alternaria brassicae" "Kuntze, 1898" 2
"Dichotomomyces cejpii" "Aspergillus cejpii" "Scott, 1970" 2
"Dickeya dieffenbachiae" "Dickeya dadantii dieffenbachiae" "Samson et al., 2005" 1
@ -3938,7 +3938,7 @@
"Diplodina pedicularis" "Leptosphaeria pedicularis" "Lind, 1924" 2
"Diplodinium lunula" "Gymnodinium lunula" "Klebs, 1912" 3
"Diplodinium uncinata" "Blepharocorys uncinata" "Fiorentini, 1890" 3
"Diplogonoporus balaenopterae" "Diphyllobothrium balaenopterae" "Lonnberg, 1892" 3
"Diplogonoporus balaenopterae" "Diphyllobothrium balaenopterae" "Lonnberg, 1892" 2
"Diplophrys stercorea" "Sorodiplophrys stercorea" "Cienk, 1876" 3
"Diplophysa saprolegniae" "Olpidiopsis saprolegniae" "Schrot, 1886" 3
"Diploplenodomus piskorzii" "Phoma piskorzii" "Petr, 1923" 2
@ -4105,7 +4105,7 @@
"Drechslera spicifera" "Curvularia spicifera" "Arx, 1975" 2
"Drechslera subpapendorfii" "Curvularia subpapendorfii" "Mouch, 1975" 2
"Drechslera tripogonis" "Curvularia tripogonis" "Patil et al., 1972" 2
"Drepanidotaenia dusmeti" "Hymenolepis dusmeti" "Lopez-Neyra, 1942" 3
"Drepanidotaenia dusmeti" "Hymenolepis dusmeti" "Lopez-Neyra, 1942" 2
"Drepanomonas simulans" "Microthorax simulans" "Kahl, 1926" 3
"Drulanta edenshawi" "Parahsuum edenshawi" "Carter, 1988" 3
"Drulanta mostleri" "Parahsuum mostleri" "Yeh, 1987" 3
@ -4174,8 +4174,8 @@
"Eidamia viridescens" "Trichoderma viridescens" "Horne et al., 1923" 2
"Eilohedra weddellensis" "Alabaminella weddellensis" "Earland, 1936" 3
"Electothigma acuminatus" "Metopus acuminatus" "Jankowski, 1967" 3
"Elizabethkingia anophelis endophytica" "Elizabethkingia anophelis" "Garcia-Lopez et al., 2020" 3
"Elizabethkingia endophytica" "Elizabethkingia anophelis" "Kampfer et al., 2015" 3
"Elizabethkingia anophelis endophytica" "Elizabethkingia anophelis" "Garcia-Lopez et al., 2020" 2
"Elizabethkingia endophytica" "Elizabethkingia anophelis" "Kampfer et al., 2015" 2
"Elkelangia" "Novosphingopyxis" "Hordt et al., 2020" 2
"Elkelangia baekryungensis" "Novosphingopyxis baekryungensis" "Hordt et al., 2020" 2
"Ellipsolagena bidens" "Parafissurina bidens" "Cushman, 1930" 3
@ -4255,7 +4255,7 @@
"Emericella spectabilis" "Aspergillus spectabilis" "Chr, 1978" 2
"Emericella unguis" "Aspergillus unguis" "Malloch et al., 1972" 2
"Emmonsia crescens" "Ajellomyces crescens" "Emmons et al., 1960" 3
"Empedobacter falsenii" "Wautersiella falsenii" "Zhang et al., 2014" 3
"Empedobacter falsenii" "Wautersiella falsenii" "Zhang et al., 2014" 2
"Enantiocristellaria navicula" "Saracenaria navicula" "DOrbigny, 1840" 3
"Encephalitozoon cuniculi" "Nosema cuniculi" "Levaditi et al., 1923" 3
"Encephalitozoon ixodis" "Unikaryon ixodis" "Weiser et al., 1975" 3
@ -4341,7 +4341,7 @@
"Enteridium splendens" "Reticularia splendens" "TMacbr, 1899" 3
"Enterobacter aerogenes" "Klebsiella aerogenes" "Hormaeche et al., 1960" 1
"Enterobacter agglomerans" "Pantoea agglomerans" "Ewing et al., 1972" 1
"Enterobacter amnigenus" "Lelliottia amnigena" "Izard et al., 1981" 1
"Enterobacter amnigenus" "Lelliottia amnigena" "Izard et al., 1981" 2
"Enterobacter arachidis" "Kosakonia arachidis" "Madhaiyan et al., 2010" 1
"Enterobacter cowanii" "Kosakonia cowanii" "Inoue et al., 2001" 1
"Enterobacter dissolvens" "Enterobacter cloacae dissolvens" "Brenner et al., 1988" 1
@ -4352,7 +4352,7 @@
"Enterobacter massiliensis" "Metakosakonia massiliensis" "Lagier et al., 2014"
"Enterobacter massiliensis" "Phytobacter massiliensis" "Lagier et al., 2014" 1
"Enterobacter muelleri" "Enterobacter asburiae" "Kampfer et al., 2015" 1
"Enterobacter nimipressuralis" "Lelliottia nimipressuralis" "Brenner et al., 1988" 1
"Enterobacter nimipressuralis" "Lelliottia nimipressuralis" "Brenner et al., 1988" 2
"Enterobacter oligotrophica" "Enterobacter oligotrophicus" "Akita et al., 2020" 1
"Enterobacter oryzae" "Kosakonia oryzae" "Peng et al., 2009" 1
"Enterobacter oryzendophyticus" "Kosakonia oryzendophytica" "Hardoim et al., 2015" 1
@ -4527,7 +4527,7 @@
"Erwinia herbicola" "Pantoea agglomerans" "Dye, 1964" 1
"Erwinia milletiae" "Pantoea agglomerans" "Magrou, 1937" 1
"Erwinia nigrifluens" "Brenneria nigrifluens" "Wilson et al., 1957" 1
"Erwinia nimipressuralis" "Lelliottia nimipressuralis" "Dye, 1969" 1
"Erwinia nimipressuralis" "Lelliottia nimipressuralis" "Dye, 1969" 2
"Erwinia paradisiaca" "Dickeya paradisiaca" "Fernandez-Borrero et al., 1970" 1
"Erwinia persicinus" "Erwinia persicina" "Hao et al., 1990" 1
"Erwinia quercina" "Lonsdalea quercina" "Hildebrand et al., 1967" 1
@ -4844,33 +4844,33 @@
"Flaviramulus ichthyoenteri" "Wocania ichthyoenteri" "Zhang et al., 2013" 3
"Flavirhabdus" "Lacinutrix" "Shakeela et al., 2015" 3
"Flavirhabdus iliipiscaria" "Lacinutrix iliipiscaria" "Shakeela et al., 2015" 3
"Flavobacterium anatoliense" "Myroides anatoliensis" "Kacagan et al., 2013" 3
"Flavobacterium anatoliense" "Myroides anatoliensis" "Kacagan et al., 2013" 2
"Flavobacterium balustinum" "Chryseobacterium balustinum" "Harrison, 1929" 2
"Flavobacterium bomensis" "Flavobacterium bomense" "Liu et al., 2019" 2
"Flavobacterium branchiophila" "Flavobacterium branchiophilum" "Wakabayashi et al., 1989" 2
"Flavobacterium breve" "Empedobacter brevis" "Holmes et al., 1982" 3
"Flavobacterium breve" "Empedobacter brevis" "Holmes et al., 1982" 2
"Flavobacterium capsulatum" "Novosphingobium capsulatum" "Leifson, 1962" 2
"Flavobacterium ceti" "Myroides ceti" "Vela et al., 2013" 3
"Flavobacterium cloacae" "Myroides cloacae" "Liu et al., 2017" 3
"Flavobacterium ceti" "Myroides ceti" "Vela et al., 2013" 2
"Flavobacterium cloacae" "Myroides cloacae" "Liu et al., 2017" 2
"Flavobacterium daemonensis" "Flavobacterium daemonense" "Ngo et al., 2015" 2
"Flavobacterium esteraromaticum" "Microbacterium esteraromaticum" "Bergey et al., 1930" 2
"Flavobacterium ferrugineum" "Terrimonas ferruginea" "Sickles et al., 1934" 3
"Flavobacterium ferrugineum" "Terrimonas ferruginea" "Sickles et al., 1934" 2
"Flavobacterium gleum" "Chryseobacterium gleum" "Holmes et al., 1984" 2
"Flavobacterium gondwanense" "Psychroflexus gondwanensis" "Dobson et al., 1993" 3
"Flavobacterium halmephilium" "Halomonas halmophila" "Elazari-Volcani, 1940" 1
"Flavobacterium halmophilum" "Halomonas halmophila" "Corrig Elazari-Volcani, 1940" 1
"Flavobacterium heparinum" "Pedobacter heparinus" "Payza et al., 1956" 3
"Flavobacterium heparinum" "Pedobacter heparinus" "Payza et al., 1956" 2
"Flavobacterium indologenes" "Chryseobacterium indologenes" "Yabuuchi et al., 1983" 2
"Flavobacterium indoltheticum" "Chryseobacterium indoltheticum" "Campbell et al., 1951" 2
"Flavobacterium jejuensis" "Flavobacterium jejuense" "Park et al., 2016" 2
"Flavobacterium johnsonae" "Flavobacterium johnsoniae" "Bernardet et al., 1996" 2
"Flavobacterium kyungheensis" "Flavobacterium kyungheense" "Son et al., 2014" 2
"Flavobacterium marinotypicum" "Microbacterium maritypicum" "ZoBell et al., 1944" 2
"Flavobacterium marinum" "Myroides aquimaris" "Song et al., 2013" 3
"Flavobacterium meningosepticum" "Elizabethkingia meningoseptica" "King, 1959" 3
"Flavobacterium mizutaii" "Sphingobacterium mizutaii" "Holmes et al., 1988" 3
"Flavobacterium multivorum" "Sphingobacterium multivorum" "Holmes et al., 1981" 3
"Flavobacterium odoratum" "Myroides odoratus" "Stutzer, 1929" 3
"Flavobacterium marinum" "Myroides aquimaris" "Song et al., 2013" 2
"Flavobacterium meningosepticum" "Elizabethkingia meningoseptica" "King, 1959" 2
"Flavobacterium mizutaii" "Sphingobacterium mizutaii" "Holmes et al., 1988" 2
"Flavobacterium multivorum" "Sphingobacterium multivorum" "Holmes et al., 1981" 2
"Flavobacterium odoratum" "Myroides odoratus" "Stutzer, 1929" 2
"Flavobacterium okeanokoites" "Planomicrobium okeanokoites" "ZoBell et al., 1944"
"Flavobacterium okeanokoites" "Planococcus okeanokoites" "ZoBell et al., 1944" 2
"Flavobacterium qiangtangensis" "Flavobacterium qiangtangense" "Huang et al., 2015" 2
@ -4878,12 +4878,12 @@
"Flavobacterium salegens" "Salegentibacter salegens" "Dobson et al., 1993" 3
"Flavobacterium scophthalmum" "Chryseobacterium scophthalmum" "Mudarris et al., 1994" 2
"Flavobacterium spartansii" "Flavobacterium tructae" "Loch et al., 2019" 2
"Flavobacterium spiritivorum" "Sphingobacterium spiritivorum" "Holmes et al., 1982" 3
"Flavobacterium spiritivorum" "Sphingobacterium spiritivorum" "Holmes et al., 1982" 2
"Flavobacterium tangerina" "Flavobacterium tangerinum" "Li et al., 2020" 2
"Flavobacterium thalpophilum" "Sphingobacterium thalpophilum" "Holmes et al., 1983" 3
"Flavobacterium thalpophilum" "Sphingobacterium thalpophilum" "Holmes et al., 1983" 2
"Flavobacterium uliginosum" "Zobellia uliginosa" "ZoBell et al., 1944" 3
"Flavobacterium viscosus" "Flavobacterium viscosum" "Li et al., 2020" 2
"Flavobacterium yabuuchiae" "Sphingobacterium spiritivorum" "Holmes et al., 1988" 3
"Flavobacterium yabuuchiae" "Sphingobacterium spiritivorum" "Holmes et al., 1988" 2
"Flavobacterium zhairuonensis" "Flavobacterium zhairuonense" "Debnath et al., 2020" 2
"Flectobacillus glomeratus" "Polaribacter glomeratus" "McGuire et al., 1988" 3
"Flectobacillus marinus" "Cyclobacterium marinum" "Borrall et al., 1978" 3
@ -4895,8 +4895,8 @@
"Flexibacter filiformis" "Chitinophaga filiformis" "Reichenbach, 1989" 3
"Flexibacter japonensis" "Chitinophaga japonensis" "Fujita et al., 1997" 3
"Flexibacter litoralis" "Bernardetia litoralis" "Lewin, 1969" 3
"Flexibacter maritimus" "Tenacibaculum maritimum" "Wakabayashi et al., 1989" 3
"Flexibacter ovolyticus" "Tenacibaculum ovolyticum" "Hansen et al., 1992" 3
"Flexibacter maritimus" "Tenacibaculum maritimum" "Wakabayashi et al., 1989" 2
"Flexibacter ovolyticus" "Tenacibaculum ovolyticum" "Hansen et al., 1992" 2
"Flexibacter polymorphus" "Garritya polymorpha" "Lewin, 1974" 3
"Flexibacter psychrophilus" "Flavobacterium psychrophilum" "Bernardet et al., 1989" 2
"Flexibacter roseolus" "Hugenholtzia roseola" "Lewin et al., 2016" 3
@ -5338,7 +5338,7 @@
"Gordonia rubropertinctus" "Gordonia rubripertincta" "Stackebrandt et al., 1989" 2
"Gordonibacter faecihominis" "Gordonibacter urolithinfaciens" "Jin et al., 2015" 2
"Gottfriedia acidiceler" "Gottfriedia acidiceleris" "Gupta et al., 2020" 2
"Grabhamia australis" "Aedes australis" "Strickland, 1911" 3
"Grabhamia australis" "Aedes australis" "Strickland, 1911" 2
"Grahamella" "Bartonella" "Ristic et al., 1984" 2
"Grahamella peromysci" "Bartonella peromysci" "Ristic et al., 1984" 2
"Grahamella talpae" "Bartonella talpae" "Ristic et al., 1984" 2
@ -5486,20 +5486,20 @@
"Haloarcobacter ebronensis" "Halarcobacter ebronensis" "Perez-Cataluna et al., 2019"
"Haloarcobacter ebronensis" "Arcobacter ebronensis" "Perez-Cataluna et al., 2019" 2
"Haloarcula mukohataei" "Halomicrobium mukohataei" "Ihara et al., 1997" 3
"Halobacterium cutirubrum" "Halobacterium salinarum" "Elazari-Volcani, 1957" 3
"Halobacterium cutirubrum" "Halobacterium salinarum" "Elazari-Volcani, 1957" 2
"Halobacterium denitrificans" "Haloferax denitrificans" "Tomlinson et al., 1986" 3
"Halobacterium distributum" "Halorubrum distributum" "Zvyagintseva et al., 1989" 3
"Halobacterium distributus" "Halorubrum distributum" "Zvyagintseva et al., 1989" 3
"Halobacterium halobium" "Halobacterium salinarum" "Elazari-Volcani, 1957" 3
"Halobacterium halobium" "Halobacterium salinarum" "Elazari-Volcani, 1957" 2
"Halobacterium lacusprofundi" "Halorubrum lacusprofundi" "Franzmann et al., 1989" 3
"Halobacterium mediterranei" "Haloferax mediterranei" "Rodriguez-Valera et al., 1983" 3
"Halobacterium pharaonis" "Natronomonas pharaonis" "Soliman et al., 1983" 3
"Halobacterium piscisalsi" "Halobacterium salinarum" "Yachai et al., 2008" 3
"Halobacterium piscisalsi" "Halobacterium salinarum" "Yachai et al., 2008" 2
"Halobacterium saccharovorum" "Halorubrum saccharovorum" "Tomlinson et al., 1977" 3
"Halobacterium salinarium" "Halobacterium salinarum" "Elazari-Volcani, 1957" 3
"Halobacterium salinarium" "Halobacterium salinarum" "Elazari-Volcani, 1957" 2
"Halobacterium sodomense" "Halorubrum sodomense" "Oren, 1983" 3
"Halobacterium trapanicum" "Halorubrum trapanicum" "Elazari-Volcani, 1957" 3
"Halobacterium vallismortis" "Haloarcula vallismortis" "Gonzalez et al., 1979" 3
"Halobacterium vallismortis" "Haloarcula vallismortis" "Gonzalez et al., 1979" 2
"Halobacterium volcanii" "Haloferax volcanii" "Mullakhanbhai et al., 1975" 3
"Halobacteroides acetoethylicus" "Halanaerobium acetethylicum" "Rengpipat et al., 1989" 2
"Halobacteroides lacunaris" "Halanaerobacter lacunarum" "Zhilina et al., 1992" 2
@ -5780,7 +5780,7 @@
"Hendersonia pinicola" "Hendersonula pinicola" "Trotter, 1972" 2
"Hendersonia symploci" "Hendersonula symploci" "Berk et al., 1873" 2
"Hennebertia ovalis" "Wardomyces ovalis" "Morelet, 1969" 3
"Hepatiarius longissimus" "Opisthorchis longissimus" "Feizullaev, 1961" 3
"Hepatiarius longissimus" "Opisthorchis longissimus" "Feizullaev, 1961" 2
"Heptameria acuta" "Leptosphaeria acuta" "Cooke, 1889" 2
"Heptameria albopunctata" "Leptosphaeria albopunctata" "Cooke, 1889" 2
"Heptameria artemisiae" "Leptosphaeria artemisiae" "Cooke, 1889" 2
@ -5853,7 +5853,7 @@
"Heteroconium chaetospira" "Cladophialophora chaetospira" "Ellis, 1976" 2
"Heterolepa haidingeri" "Cibicides haidingeri" "DOrbigny, 1846" 3
"Heteropatellina frustratiformis" "Ungulatelloides frustratiformis" "McCulloch, 1977" 3
"Heterophyes yokogawai" "Metagonimus yokogawai" "Katsurada, 1912" 3
"Heterophyes yokogawai" "Metagonimus yokogawai" "Katsurada, 1912" 2
"Heterospiroloculina bikiniensis" "Inaequalina bikiniensis" "McCulloch, 1977" 3
"Heterospiroloculina culebraensis" "Inaequalina culebraensis" "McCulloch, 1977" 3
"Heterosporium algarum" "Cladosporium algarum" "Cooke et al., 1890" 2
@ -5972,8 +5972,8 @@
"Huaishuia" "Celeribacter" "Wang et al., 2012" 2
"Huaishuia halophila" "Celeribacter halophilus" "Wang et al., 2012" 2
"Hughesiella euricoi" "Ceratocystis euricoi" "Bat et al., 1956" 3
"Hulecoeteomyia fluviatilis" "Aedes fluviatilis" "Leicester, 1908" 3
"Hulecoeteomyia milsoni" "Aedes milsoni" "Taylor, 1916" 3
"Hulecoeteomyia fluviatilis" "Aedes fluviatilis" "Leicester, 1908" 2
"Hulecoeteomyia milsoni" "Aedes milsoni" "Taylor, 1916" 2
"Humicoccus" "Nakamurella" "Yoon et al., 2007" 2
"Humicoccus flavidus" "Nakamurella flavida" "Yoon et al., 2007" 2
"Humicola minima" "Ochroconis minima" "Fassat, 1967" 2
@ -6942,7 +6942,7 @@
"Leifsonia pindariensis" "Microterricola pindariensis" "Reddy et al., 2008" 2
"Leiotrocha serpularum" "Cyclochaeta serpularum" "Fabre-Domergue, 1888" 3
"Leisingera nanhaiensis" "Sedimentitalea nanhaiensis" "Sun et al., 2014" 2
"Lelliottia aquatilis" "Lelliottia jeotgali" "Kampfer et al., 2018" 1
"Lelliottia aquatilis" "Lelliottia jeotgali" "Kampfer et al., 2018" 2
"Lembus armatus" "Philasterides armatus" "Kahl, 1926" 3
"Lembus kenti" "Cohnilembus kenti" "Kahl, 1931" 3
"Lembus pusillus" "Pseudocohnilembus pusillus" "Quennerstedt, 1869" 3
@ -7208,7 +7208,7 @@
"Lonsdalea quercina iberica" "Lonsdalea iberica" "Brady et al., 2012" 1
"Lonsdalea quercina populi" "Lonsdalea populi" "Toth et al., 2013" 1
"Lonsdalea quercina quercina" "Lonsdalea quercina" "Brady et al., 2012" 1
"Loossia dobrogiensis" "Metagonimus dobrogiensis" "Ciurea, 1915" 3
"Loossia dobrogiensis" "Metagonimus dobrogiensis" "Ciurea, 1915" 2
"Lophocorys neatum" "Lophocyrtis neatum" "Sanfilippo, 1990" 3
"Lophophyton gallinae" "Microsporum gallinae" "Matr et al., 1899" 3
"Loxocephalus colpidiopsis" "Dexiotricha colpidiopsis" "Kahl, 1926" 3
@ -7490,7 +7490,7 @@
"Mesoflavibacter sabulilitoris" "Mesoflavibacter zeaxanthinifaciens sabulilitoris" "Park et al., 2014" 3
"Mesomycoplasma molaris" "Mesomycoplasma molare" "Gupta et al., 2018" 3
"Mesonia maritimus" "Mesonia maritima" "Sung et al., 2017" 3
"Mesoplasma pleciae" "Acholeplasma pleciae" "Tully et al., 1994" 3
"Mesoplasma pleciae" "Acholeplasma pleciae" "Tully et al., 1994" 2
"Metacarinina charlesensis" "Laticarinina charlesensis" "McCulloch, 1977" 3
"Metacarinina chathamensis" "Laticarinina chathamensis" "McCulloch, 1977" 3
"Metacarinina hoodensis" "Laticarinina hoodensis" "McCulloch, 1977" 3
@ -7882,7 +7882,7 @@
"Monosporium sclerotiale" "Scedosporium sclerotiale" "Pepere, 1914" 3
"Monosporium sepedonioides" "Chrysosporium sepedonioides" "Harz, 1872" 3
"Moorella thermoautotrophica" "Moorella thermoacetica" "Collins et al., 1994" 2
"Moraxella anatipestifer" "Riemerella anatipestifer" "Bruner et al., 1954" 3
"Moraxella anatipestifer" "Riemerella anatipestifer" "Bruner et al., 1954" 2
"Moraxella phenylpyruvica" "Psychrobacter phenylpyruvicus" "Bovre et al., 1967" 1
"Moraxella urethralis" "Oligella urethralis" "Lautrop et al., 1970" 2
"Morella entamoebae" "Sphaerita entamoebae" "Perez Reyes, 1964" 3
@ -7898,7 +7898,7 @@
"Mrazekia niphargi" "Microsporidium niphargi" "Poisson, 1924" 3
"Mrazekia piscicola" "Jirovecia piscicola" "Cepede, 1924" 3
"Mrazekia tetraspora" "Scipionospora tetraspora" "Leger et al., 1922" 3
"Mucidus africanus" "Aedes africanus" "Theobald, 1901" 3
"Mucidus africanus" "Aedes africanus" "Theobald, 1901" 2
"Mucor angarensis" "Circinella angarensis" "Schostak, 1897" 3
"Mucor arrhizus" "Rhizopus arrhizus" "Hagem, 1908" 2
"Mucor assamensis" "Hyphomucor assamensis" "Mehrotra et al., 1970" 3
@ -7926,7 +7926,7 @@
"Muricauda antarctica" "Muricauda taeanensis" "Wu et al., 2013" 3
"Muricauda lutea" "Croceivirga lutea" "Wang et al., 2017" 3
"Muriicola lacisalsi" "Maritimibacter lacisalsi" "Wang et al., 2021" 2
"Musca azurea" "Lucilia azurea" "Doleschall, 1858" 3
"Musca azurea" "Lucilia azurea" "Doleschall, 1858" 2
"Mya nitens" "Ervilia nitens" "Montagu, 1808" 3
"Myceloblastanon albicans" "Candida albicans" "Ota, 1927" 2
"Myceloblastanon guilliermondii" "Meyerozyma guilliermondii" "Ota, 1927" 3
@ -8221,7 +8221,7 @@
"Mycterotrix ovata" "Maryna ovata" "Gelei, 1950" 3
"Myllocercion rhodanon" "Schadelfusslerus rhodanon" "Foreman, 1968" 3
"Myrionecta rubrum" "Mesodinium rubrum" "Jankowski, 1976" 3
"Myroides xuanwuensis" "Myroides odoratimimus xuanwuensis" "Zhang et al., 2014" 3
"Myroides xuanwuensis" "Myroides odoratimimus xuanwuensis" "Zhang et al., 2014" 2
"Myxococcus coralloides" "Corallococcus coralloides" "Thaxter, 1892" 2
"Myxococcus disciformis" "Archangium disciforme" "Thaxter, 1904" 2
"Myxococcus flavescens" "Myxococcus virescens" "Yamanaka et al., 1990" 2
@ -8231,8 +8231,8 @@
"Myxotrichum johnstonii" "Gymnoascus johnstonii" "Massee et al., 1902" 3
"Myzocytium humicola" "Myzocytiopsis humicola" "Barron et al., 1975" 3
"Myzocytium vermicola" "Myzocytiopsis vermicola" "Fisch, 1892" 3
"Myzorhynchus minutus" "Anopheles minutus" "Theobald, 1903" 3
"Myzorhynchus pallidus" "Anopheles pallidus" "Swellengrebel, 1919" 3
"Myzorhynchus minutus" "Anopheles minutus" "Theobald, 1903" 2
"Myzorhynchus pallidus" "Anopheles pallidus" "Swellengrebel, 1919" 2
"Mzabimyces" "Halopolyspora" "Saker et al., 2015" 2
"Mzabimyces algeriensis" "Halopolyspora algeriensis" "Saker et al., 2015" 2
"Naematelia aurantia" "Tremella aurantia" "Burt, 1921" 3
@ -9265,8 +9265,8 @@
"Orcadella operculata" "Licea operculata" "Wingate, 1889" 3
"Orcadella parasitica" "Licea parasitica" "Hagelst, 1942" 3
"Orcadella pusilla" "Licea pusilla" "Hagelst, 1942" 3
"Oribaculum" "Porphyromonas" "Moore et al., 1994" 3
"Oribaculum catoniae" "Porphyromonas catoniae" "Moore et al., 1994" 3
"Oribaculum" "Porphyromonas" "Moore et al., 1994" 2
"Oribaculum catoniae" "Porphyromonas catoniae" "Moore et al., 1994" 2
"Ornatispora frondicola" "Stachybotrys frondicola" "Hyde et al., 1999" 2
"Ornatispora gamsii" "Stachybotrys gamsii" "Hyde et al., 1999" 2
"Ornatispora nepalensis" "Stachybotrys nepalensis" "Whitton et al., 2012" 2
@ -9602,7 +9602,7 @@
"Pedobacter huanghensis" "Daejeonella huanghensis" "Qiu et al., 2014" 3
"Pedobacter luteus" "Daejeonella lutea" "Oh et al., 2013" 3
"Pedobacter oryzae" "Daejeonella oryzae" "Jeon et al., 2009" 3
"Pedobacter piscium" "Pedobacter antarcticus" "Steyn et al., 2014" 3
"Pedobacter piscium" "Pedobacter antarcticus" "Steyn et al., 2014" 2
"Pedobacter ruber" "Daejeonella rubra" "Margesin et al., 2013" 3
"Pedobacter saltans" "Pseudopedobacter saltans" "Steyn et al., 1998" 3
"Pedobacter tournemirensis" "Arcticibacter tournemirensis" "Urios et al., 2013" 3
@ -9828,7 +9828,7 @@
"Petersenia andreei" "Sirolpidium andreei" "Sparrow, 1936" 3
"Petersenia catenophlyctidis" "Cornumyces catenophlyctidis" "Sundaram, 1968" 3
"Petersenia irregularis" "Cornumyces irregularis" "Sparrow, 1943" 3
"Petraeus vignei" "Giardia vignei" "Rochebrune, 1882" 3
"Petraeus vignei" "Giardia vignei" "Rochebrune, 1882" 2
"Petriella boulangeri" "Microascus boulangeri" "Curzi, 1930" 3
"Petriellidium boydii" "Pseudallescheria boydii" "Malloch, 1970" 2
"Petriellidium desertorum" "Scedosporium desertorum" "Arx et al., 1973" 3
@ -9850,8 +9850,8 @@
"Phacellium geranii" "Graphium geranii" "Braun, 1993" 3
"Phacellium ligulariae" "Graphium ligulariae" "Braun, 1993" 3
"Phacellium trifolii" "Graphium trifolii" "Braun, 1993" 3
"Phaenicia azurea" "Lucilia azurea" "Robineau-Desvoidy, 1863" 3
"Phaenicia pallescens" "Lucilia pallescens" "Shannon, 1924" 3
"Phaenicia azurea" "Lucilia azurea" "Robineau-Desvoidy, 1863" 2
"Phaenicia pallescens" "Lucilia pallescens" "Shannon, 1924" 2
"Phaenicosphaera mammilla" "Hegleria mammilla" "Sheng et al., 1985" 3
"Phaeobacter aquaemixtae" "Leisingera aquaemixtae" "Park et al., 2014" 2
"Phaeobacter arcticus" "Pseudophaeobacter arcticus" "Zhang et al., 2008" 2
@ -9895,7 +9895,7 @@
"Phloeophthora syringae" "Phytophthora syringae" "Kleb, 1906" 3
"Phloeospora trifolii" "Leptosphaeria trifolii" "Cavara, 1878" 2
"Phlyctospora persoonii" "Elaphomyces persoonii" "Corda, 1854" 3
"Phocaeicola chinchillae" "Phocaeicola sartorii" "Garcia-Lopez et al., 2020" 3
"Phocaeicola chinchillae" "Phocaeicola sartorii" "Garcia-Lopez et al., 2020" 2
"Phoma acuta" "Leptosphaeria acuta" "Fuckel, 1870" 2
"Phoma errabunda" "Leptosphaeria errabunda" "Desm, 1849" 2
"Phoma macrocapsa" "Leptosphaeria macrocapsa" "Trail, 1886" 2
@ -10127,7 +10127,7 @@
"Plagiotricha camelus" "Trichoda camelus" "Bory, 1824" 3
"Plagiotricha sinuata" "Trichoda sinuata" "Bory, 1824" 3
"Plagiotricha succisa" "Psilotricha succisa" "Bory, 1824" 3
"Planaria punctata" "Fasciola punctata" "Muller, 1776" 3
"Planaria punctata" "Fasciola punctata" "Muller, 1776" 2
"Planctomyces brasiliensis" "Rubinisphaera brasiliensis" "Schlesner, 1990" 3
"Planctomyces limnophilus" "Planctopirus limnophila" "Hirsch et al., 1986" 3
"Planctomyces maris" "Gimesia maris" "Bauld et al., 1980" 3
@ -10432,8 +10432,8 @@
"Porphyrobacter mercurialis" "Croceibacterium mercuriale" "Coil et al., 2016" 2
"Porphyrobacter neustonensis" "Erythrobacter neustonensis" "Fuerst et al., 2020" 2
"Porphyrobacter sanguineus" "Erythrobacter sanguineus" "Hiraishi et al., 2002" 2
"Porphyromonas cansulci" "Porphyromonas crevioricanis" "Collins et al., 1994" 3
"Porphyromonas salivosa" "Porphyromonas macacae" "Love et al., 1992" 3
"Porphyromonas cansulci" "Porphyromonas crevioricanis" "Collins et al., 1994" 2
"Porphyromonas salivosa" "Porphyromonas macacae" "Love et al., 1992" 2
"Posadasia esteriformis" "Coccidioides esteriformis" "Canton, 1898" 3
"Poseidonibacter lekithochrous" "Arcobacter lekithochrous" "Perez-Cataluna et al., 2019" 2
"Pottsiocles hannae" "Manuelophrya hannae" "Guhl, 1985" 3
@ -10450,7 +10450,7 @@
"Prauserella flava" "Prauserella salsuginis" "Li et al., 2009" 2
"Prevotella oulora" "Prevotella oulorum" "Shah et al., 1990" 2
"Prevotella ruminicola brevis" "Prevotella brevis" "Shah et al., 1990" 2
"Prevotella tannerae" "Alloprevotella tannerae" "Moore et al., 1994" 3
"Prevotella tannerae" "Alloprevotella tannerae" "Moore et al., 1994" 2
"Prevotella zoogleoformans" "Capsularis zoogleoformans" "Shah et al., 1994" 3
"Primorskyibacter insulae" "Pseudoprimorskyibacter insulae" "Park et al., 2015" 2
"Procandida albicans" "Candida albicans" "Novak et al., 1961" 2
@ -11111,7 +11111,7 @@
"Rectocibicidella robertsi" "Dyocibicides robertsi" "McLean, 1956" 3
"Rectoglandulina rotundata" "Pseudonodosaria rotundata" "Reuss, 1850" 3
"Recurvoides trochamminiformis" "Recurvoidatus trochamminiformis" "Saidova, 1961" 3
"Reedomyia sudanensis" "Aedes sudanensis" "Theobald, 1913" 3
"Reedomyia sudanensis" "Aedes sudanensis" "Theobald, 1913" 2
"Reichenbachia" "Reichenbachiella" "Nedashkovskaya et al., 2003" 3
"Reichenbachia agariperforans" "Reichenbachiella agariperforans" "Nedashkovskaya et al., 2003" 3
"Remaneica gonzalezi" "Remaneicella gonzalezi" "Seiglie, 1964" 3
@ -11462,7 +11462,7 @@
"Rotalina truncatulinoides" "Globorotalia truncatulinoides" "DOrbigny, 1839" 3
"Rotamorphina minuta" "Valvulineria minuta" "Schubert, 1904" 3
"Rothia dentocariosus" "Rothia dentocariosa" "Georg et al., 1967" 2
"Roubaudiella caerulea" "Lucilia caerulea" "Seguy, 1925" 3
"Roubaudiella caerulea" "Lucilia caerulea" "Seguy, 1925" 2
"Rozella itersoniliae" "Pleotrachelus itersoniliae" "Barr et al., 1980" 3
"Rozella septigena" "Rozellopsis septigena" "Cornu, 1872" 3
"Rozella simulans" "Rozellopsis simulans" "Fisch, 1882" 3
@ -11790,16 +11790,16 @@
"Septotrochammina gonzalezi" "Remaneicella gonzalezi" "Seiglie, 1964" 3
"Serpens" "Pseudomonas" "Hespell, 1977" 1
"Serpens flexibilis" "Pseudomonas flexibilis" "Hespell, 1977" 1
"Serpula" "Brachyspira" "Stanton et al., 1991" 3
"Serpula hyodysenteriae" "Brachyspira hyodysenteriae" "Stanton et al., 1991" 3
"Serpula innocens" "Brachyspira innocens" "Stanton et al., 1991" 3
"Serpulina" "Brachyspira" "Stanton, 1992" 3
"Serpulina alvinipulli" "Brachyspira alvinipulli" "Stanton et al., 1998" 3
"Serpulina hyodysenteriae" "Brachyspira hyodysenteriae" "Stanton et al., 1992" 3
"Serpulina innocens" "Brachyspira innocens" "Stanton et al., 1992" 3
"Serpulina intermedia" "Brachyspira intermedia" "Stanton et al., 1997" 3
"Serpulina murdochii" "Brachyspira murdochii" "Stanton et al., 1997" 3
"Serpulina pilosicoli" "Brachyspira pilosicoli" "Trott et al., 1996" 3
"Serpula" "Brachyspira" "Stanton et al., 1991" 2
"Serpula hyodysenteriae" "Brachyspira hyodysenteriae" "Stanton et al., 1991" 2
"Serpula innocens" "Brachyspira innocens" "Stanton et al., 1991" 2
"Serpulina" "Brachyspira" "Stanton, 1992" 2
"Serpulina alvinipulli" "Brachyspira alvinipulli" "Stanton et al., 1998" 2
"Serpulina hyodysenteriae" "Brachyspira hyodysenteriae" "Stanton et al., 1992" 2
"Serpulina innocens" "Brachyspira innocens" "Stanton et al., 1992" 2
"Serpulina intermedia" "Brachyspira intermedia" "Stanton et al., 1997" 2
"Serpulina murdochii" "Brachyspira murdochii" "Stanton et al., 1997" 2
"Serpulina pilosicoli" "Brachyspira pilosicoli" "Trott et al., 1996" 2
"Serratia glossinae" "Serratia fonticola" "Geiger et al., 2010" 1
"Serratia marcescens sakuensis" "Serratia marcescens" "Ajithkumar et al., 2003" 1
"Serratia marinorubra" "Serratia rubidaea" "ZoBell et al., 1944" 1
@ -12111,12 +12111,12 @@
"Sphaerulina amicta" "Appendichordella amicta" "Kohlm, 1962" 3
"Sphaerulina tanaceti" "Leptosphaeria tanaceti" "Shoemaker, 1976" 2
"Sphinctocystis elliptica" "Cymatopleura elliptica" "Kuntze" 3
"Sphingobacterium antarcticum" "Pedobacter antarcticus" "Shivaji et al., 1992" 3
"Sphingobacterium antarcticus" "Pedobacter antarcticus" "Shivaji et al., 1992" 3
"Sphingobacterium heparinum" "Pedobacter heparinus" "Takeuchi et al., 1993" 3
"Sphingobacterium mizutae" "Sphingobacterium mizutaii" "Yabuuchi et al., 1983" 3
"Sphingobacterium pakistanensis" "Sphingobacterium pakistanense" "Ahmed et al., 2015" 3
"Sphingobacterium piscium" "Pedobacter antarcticus" "Takeuchi et al., 1993" 3
"Sphingobacterium antarcticum" "Pedobacter antarcticus" "Shivaji et al., 1992" 2
"Sphingobacterium antarcticus" "Pedobacter antarcticus" "Shivaji et al., 1992" 2
"Sphingobacterium heparinum" "Pedobacter heparinus" "Takeuchi et al., 1993" 2
"Sphingobacterium mizutae" "Sphingobacterium mizutaii" "Yabuuchi et al., 1983" 2
"Sphingobacterium pakistanensis" "Sphingobacterium pakistanense" "Ahmed et al., 2015" 2
"Sphingobacterium piscium" "Pedobacter antarcticus" "Takeuchi et al., 1993" 2
"Sphingobium algicola" "Sphingobium limneticum" "Lee et al., 2017" 2
"Sphingobium barthaii" "Sphingobium fuliginis" "Maeda et al., 2015" 2
"Sphingobium chinhatense" "Sphingobium indicum" "Dadhwal et al., 2020" 2
@ -12415,7 +12415,7 @@
"Staurosphaera pusilla" "Stigmosphaerostylus pusilla" "Hinde, 1899" 3
"Staurosphaera sedecimporata" "Emiluvia sedecimporata" "Rust, 1885" 3
"Staurosphaera trispinosa" "Staurolonche trispinosa" "Kozur et al., 1979" 3
"Stegomyia wellmanii" "Aedes wellmanii" "Theobald, 1910" 3
"Stegomyia wellmanii" "Aedes wellmanii" "Theobald, 1910" 2
"Steinia balladynula" "Oxytricha balladynula" "Kahl, 1932" 3
"Steinia candens" "Cyrtohymena candens" "Kahl, 1932" 3
"Steinia citrina" "Cyrtohymena citrina" "Berger et al., 1987" 3
@ -12487,7 +12487,7 @@
"Stemphylium uredinis" "Alternaria uredinis" "Thirum, 1947" 2
"Stenella gynoxidicola" "Cladosporium gynoxidicola" "Mulder, 1982" 2
"Stenopterobia delicatissima" "Surirella delicatissima" "Van Heurck, 1896" 3
"Stenoscutus africanus" "Aedes africanus" "Theobald, 1909" 3
"Stenoscutus africanus" "Aedes africanus" "Theobald, 1909" 2
"Stenothermobacter" "Nonlabens" "Lau et al., 2006" 3
"Stenothermobacter spongiae" "Nonlabens spongiae" "Lau et al., 2006" 3
"Stenotrophomonas africana" "Stenotrophomonas maltophilia" "Drancourt et al., 1997" 1
@ -12889,7 +12889,7 @@
"Strombidium viride" "Limnostrombidium viride" "Kahl, 1932" 3
"Strombilidium tonsuratum" "Strobilidium tonsuratum" "Meunier, 1907" 3
"Strongylidium wilberti" "Hemiamphisiella wilberti" "Foissner, 1982" 3
"Strophalosia warwicki" "Capillaria warwicki" "Maxwell, 1954" 3
"Strophalosia warwicki" "Capillaria warwicki" "Maxwell, 1954" 2
"Stylocapsa catenarum" "Plicaforacapsa catenarum" "Matsuoka, 1982" 3
"Stylocapsa oblongula" "Kilinora oblongula" "Kocher, 1981" 3
"Stylocapsa spiralis" "Kilinora spiralis" "Matsuoka, 1982" 3
@ -12986,7 +12986,7 @@
"Tachysoma siseris" "Oxytricha siseris" "Stiller, 1974" 3
"Tachysoma tricornis" "Oxytricha tricornis" "Milne, 1886" 3
"Taeniolella boppii" "Cladophialophora boppii" "Borelli, 1983" 2
"Taeniorhynchus africanus" "Aedes africanus" "Neveu-Lemaire, 1906" 3
"Taeniorhynchus africanus" "Aedes africanus" "Neveu-Lemaire, 1906" 2
"Talaromyces brevicompactus" "Hamigera brevicompactus" "Kong, 1999" 3
"Talaromyces byssochlamydoides" "Rasamsonia byssochlamydoides" "Stolk et al., 1972" 3
"Talaromyces cejpii" "Aspergillus cejpii" "Milko, 1964" 2
@ -13539,8 +13539,8 @@
"Tremella simplex" "Phaeotremella simplex" "Jacks et al., 1940" 3
"Tremella translucens" "Sirotrema translucens" "Gordon, 1938" 3
"Treponema caldaria" "Treponema caldarium" "Abt et al., 2013" 2
"Treponema hyodysenteriae" "Brachyspira hyodysenteriae" "Harris et al., 1972" 3
"Treponema innocens" "Brachyspira innocens" "Kinyon et al., 1979" 3
"Treponema hyodysenteriae" "Brachyspira hyodysenteriae" "Harris et al., 1972" 2
"Treponema innocens" "Brachyspira innocens" "Kinyon et al., 1979" 2
"Treponema stenostrepta" "Treponema stenostreptum" "Abt et al., 2013" 2
"Tretomphalus bermudezi" "Cymbaloporetta bermudezi" "Sellier de Civrieux, 1976" 3
"Tretomphalus concinnus" "Tretomphaloides concinnus" "Brady, 1884" 3
@ -14161,7 +14161,7 @@
"Wautersia paucula" "Cupriavidus pauculus" "Vaneechoutte et al., 2004" 2
"Wautersia respiraculi" "Cupriavidus respiraculi" "Vaneechoutte et al., 2004" 2
"Wautersia taiwanensis" "Cupriavidus taiwanensis" "Vaneechoutte et al., 2004" 2
"Weeksella zoohelcum" "Bergeyella zoohelcum" "Holmes et al., 1987" 3
"Weeksella zoohelcum" "Bergeyella zoohelcum" "Holmes et al., 1987" 2
"Weiseria spinosa" "Golbergia spinosa" "Golberg, 1971" 3
"Weissella jogaejeotgali" "Weissella thailandensis" "Lee et al., 2015" 2
"Weissella kimchii" "Weissella cibaria" "Choi et al., 2002" 2

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@ -276,18 +276,40 @@ MOs <- MOs %>%
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Apophysomyces",
"Arachnia", "Aspergillus", "Aureobacterium", "Aureobasidium", "Bacteroides", "Basidiobolus",
"Beauveria", "Blastocystis", "Branhamella", "Calymmatobacterium", "Candida", "Capnocytophaga",
"Catabacter", "Chaetomium", "Chryseobacterium", "Chryseomonas", "Chrysonilia", "Cladophialophora",
"Cladosporium", "Conidiobolus", "Cryptococcus", "Curvularia", "Exophiala", "Exserohilum",
"Flavobacterium", "Fonsecaea", "Fusarium", "Fusobacterium", "Hendersonula", "Hypomyces",
"Koserella", "Lelliottia", "Leptosphaeria", "Leptotrichia", "Malassezia", "Malbranchea",
"Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Nectria", "Ochroconis",
"Oidiodendron", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Prevotella", "Pseudallescheria",
"Rhizomucor", "Rhizopus", "Rhodotorula", "Scolecobasidium", "Scopulariopsis", "Scytalidium",
"Sporobolomyces", "Stachybotrys", "Stomatococcus", "Treponema", "Trichoderma", "Trichophyton",
"Trichosporon", "Tritirachium", "Ureaplasma")
| genus %in% c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes",
"Alloprevotella", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus",
"Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus",
"Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus",
"Beauveria", "Bergeyella", "Bilophilia", "Blastocystis", "Borrelia", "Brachyspira",
"Branhamella", "Brochontrix", "Brugia", "Butyricimonas", "Calymmatobacterium",
"Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cdc", "Cetobacterium",
"Chaetomium", "Chilomastix", "Chlamydia", "Chlamydophila", "Chryseobacterium",
"Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis",
"Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus",
"Demodex", "Dermatobia", "Dicrocoelium", "Dioctophyma", "Diphyllobothrium", "Dipylidium",
"Dirofilaria", "Dracunculus", "Dysgonomonas", "Echinococcus", "Echinostoma",
"Elisabethkingia", "Elizabethkingia", "Empedobacter", "Enterobius", "Enteromonas",
"Euascomycetes", "Exophiala", "Exserohilum", "Fasciola", "Fasciolopsis", "Flavobacterium",
"Fonsecaea", "Fusarium", "Fusobacterium", "Giardia", "Gnathostoma", "Haloarcula",
"Halobacterium", "Halococcus", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces",
"Hysterothylacium", "Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania",
"Lelliottia", "Leptomyxida", "Leptosphaeria", "Leptotrichia", "Loa", "Lucilia", "Lumbricus",
"Malassezia", "Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium",
"Molonomonas", "Mortierella", "Mucor", "Multiceps", "Mycocentrospora", "Mycoplasma",
"Myroides", "Nanophetus", "Nattrassia", "Necator", "Nectria", "Novospingobium", "Ochroconis",
"Odoribacter", "Oesophagostomum", "Oidiodendron", "Onchocerca", "Opisthorchis",
"Opistorchis", "Ornithobacterium", "Parabacteroides", "Paragonimus", "Paramyxovirus",
"Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola", "Phocanema", "Phoma",
"Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
"Pseudallescheria", "Pseudoterranova", "Pulex", "Retortamonas", "Rhizomucor", "Rhizopus",
"Rhodotorula", "Riemerella", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes",
"Schistosoma", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
"Spirometra", "Sporobolomyces", "Stachybotrys", "Stenotrophomononas", "Stomatococcus",
"Streptobacillus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
"Tenacibaculum", "Ternidens", "Terrimonas", "Torulopsis", "Toxocara", "Toxoplasma",
"Treponema", "Trichinella", "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton",
"Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium", "Trombicula", "Trypanosoma",
"Tunga", "Ureaplasma", "Victivallis", "Wautersiella", "Weeksella", "Wuchereria")
| rank %in% c("kingdom", "phylum", "class", "order", "family"))
~ 2,
TRUE ~ 3

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>

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</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>

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</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>
@ -224,15 +224,15 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</e
<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 11:38:23 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 3 June 2022 11:18:29 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" class="external-link">R
file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
file</a> (6.4 MB)<br>
file</a> (5.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
text file</a> (13.1 MB)<br>
@ -466,8 +466,8 @@ i.e. of column <em>‘fullname_new’</em>, see the
<code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 3 June 2022 11:18:30 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.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.old.rds" class="external-link">R

2
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</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>

2
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@ -47,7 +47,7 @@
</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>

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</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>
@ -157,16 +157,16 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.1.9011" id="amr-1819011">
<code>AMR</code> 1.8.1.9011<a class="anchor" aria-label="anchor" href="#amr-1819011"></a></h2>
<h2 class="page-header" data-toc-text="1.8.1.9012" id="amr-1819012">
<code>AMR</code> 1.8.1.9012<a class="anchor" aria-label="anchor" href="#amr-1819012"></a></h2>
<div class="section level3">
<h3 id="last-updated-june-1-8-1-9011"><small>Last updated: 3 June 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-june-1-8-1-9011"></a></h3>
<h3 id="last-updated-june-1-8-1-9012"><small>Last updated: 3 June 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-june-1-8-1-9012"></a></h3>
<div class="section level4">
<h4 id="new-1-8-1-9011">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9011"></a></h4>
<h4 id="new-1-8-1-9012">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9012"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9011">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9011"></a></h4>
<h4 id="changed-1-8-1-9012">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9012"></a></h4>
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>

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</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>
@ -210,7 +210,7 @@
<li><p><code>"V"</code> = vaginal</p></li>
</ul><p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul><li><p><code>"g"</code> = gram</p></li>
<li><p><code>"mg"</code> = milligram</p></li>
<li><p>`"mcg"`` = microgram</p></li>
<li><p><code>"mcg"</code> = microgram</p></li>
<li><p><code>"U"</code> = unit</p></li>
<li><p><code>"TU"</code> = thousand units</p></li>
<li><p><code>"MU"</code> = million units</p></li>

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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>
@ -198,7 +198,7 @@
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in variables used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p>There is one exception in variables used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: –mo–, –fullname–, –kingdom–, –phylum–, –class–, –order–, –family–, –genus–, –species–, –subspecies–, –rank–, –ref–, –species_id–, –source–, –prevalence– and –snomed–. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
</div>
@ -206,9 +206,35 @@
<h3 id="usage-of-antibiotic-group-names">Usage of antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-antibiotic-group-names"></a></h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.</p>
<p><code>r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")</code></p>
</div>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.</p><ul><li><p>–aminoglycosides–<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)</p></li>
<li><p>–aminopenicillins–<br>(amoxicillin and ampicillin)</p></li>
<li><p>–antifungals–<br>(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
<li><p>–antimycobacterials–<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)</p></li>
<li><p>–betalactams–<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>–carbapenems–<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)</p></li>
<li><p>–cephalosporins–<br>(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)</p></li>
<li><p>–cephalosporins_1st–<br>(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)</p></li>
<li><p>–cephalosporins_2nd–<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)</p></li>
<li><p>–cephalosporins_3rd–<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)</p></li>
<li><p>–cephalosporins_4th–<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)</p></li>
<li><p>–cephalosporins_5th–<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)</p></li>
<li><p>–cephalosporins_except_caz–<br>(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)</p></li>
<li><p>–fluoroquinolones–<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>–glycopeptides–<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)</p></li>
<li><p>–glycopeptides_except_lipo–<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)</p></li>
<li><p>–lincosamides–<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>–lipoglycopeptides–<br>(dalbavancin, oritavancin and telavancin)</p></li>
<li><p>–macrolides–<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>–oxazolidinones–<br>(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)</p></li>
<li><p>–penicillins–<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>–polymyxins–<br>(colistin, polymyxin B and polymyxin B/polysorbate 80)</p></li>
<li><p>–quinolones–<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>–streptogramins–<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>–tetracyclines–<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)</p></li>
<li><p>–tetracyclines_except_tgc–<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)</p></li>
<li><p>–trimethoprims–<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)</p></li>
<li><p>–ureidopenicillins–<br>(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)</p></li>
</ul></div>
</div>
<div id="stable-lifecycle">

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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>

6
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>
@ -203,7 +203,7 @@
<span class="op">)</span>
<span class="co"># S3 method for resistance_predict</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Resistance Prediction of"</span>, <span class="va">x_name</span><span class="op">)</span>,
ribbon <span class="op">=</span> <span class="cn">TRUE</span>,
@ -228,7 +228,7 @@
<dt>minimum</dt>
<dd><p>minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.</p></dd>
<dt>model</dt>
<dd><p>the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See <em>Details</em> for all valid options.</p></dd>
<dd><p>the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using <code>glm(..., family = binomial)</code>, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See <em>Details</em> for all valid options.</p></dd>
<dt>I_as_S</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values <code>"I"</code> should be treated as <code>"S"</code> (will otherwise be treated as <code>"R"</code>). The default, <code>TRUE</code>, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section <em>Interpretation of S, I and R</em> below.</p></dd>
<dt>preserve_measurements</dt>

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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9012</span>
</span>
</div>

2
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@ -59,7 +59,7 @@ Abbreviations of return values when using \code{property = "U"} (unit):
\itemize{
\item \code{"g"} = gram
\item \code{"mg"} = milligram
\item `"mcg"`` = microgram
\item \code{"mcg"} = microgram
\item \code{"U"} = unit
\item \code{"TU"} = thousand units
\item \code{"MU"} = million units

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@ -7,7 +7,7 @@
custom_eucast_rules(...)
}
\arguments{
\item{...}{rules in formula notation, see \emph{Examples}}
\item{...}{rules in \link[=`~`]{formula} notation, see \emph{Examples}}
}
\value{
A \link{list} containing the custom rules
@ -60,7 +60,7 @@ eucast_rules(df, rules = "custom", custom_rules = x)
\subsection{Using taxonomic properties in rules}{
There is one exception in variables used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: \verb{r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)}. Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}:
There is one exception in variables used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: –mo–, –fullname–, –kingdom–, –phylum–, –class–, –order–, –family–, –genus–, –species–, –subspecies–, –rank–, –ref–, –species_id–, –source–, –prevalence– and –snomed–. Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}:
\if{html}{\out{<div class="sourceCode">}}\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
@ -75,8 +75,36 @@ eucast_rules(df, rules = "custom", custom_rules = y)
\subsection{Usage of antibiotic group names}{
It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
\verb{r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\\n", collapse = "")}
\itemize{
\item –aminoglycosides–\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)
\item –aminopenicillins–\cr(amoxicillin and ampicillin)
\item –antifungals–\cr(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)
\item –antimycobacterials–\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)
\item –betalactams–\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)
\item –carbapenems–\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)
\item –cephalosporins–\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)
\item –cephalosporins_1st–\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)
\item –cephalosporins_2nd–\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)
\item –cephalosporins_3rd–\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)
\item –cephalosporins_4th–\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)
\item –cephalosporins_5th–\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)
\item –cephalosporins_except_caz–\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)
\item –fluoroquinolones–\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
\item –glycopeptides–\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)
\item –glycopeptides_except_lipo–\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)
\item –lincosamides–\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)
\item –lipoglycopeptides–\cr(dalbavancin, oritavancin and telavancin)
\item –macrolides–\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)
\item –oxazolidinones–\cr(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)
\item –penicillins–\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)
\item –polymyxins–\cr(colistin, polymyxin B and polymyxin B/polysorbate 80)
\item –quinolones–\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
\item –streptogramins–\cr(pristinamycin and quinupristin/dalfopristin)
\item –tetracyclines–\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)
\item –tetracyclines_except_tgc–\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)
\item –trimethoprims–\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)
\item –ureidopenicillins–\cr(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)
}
}
}

2
man/resistance_predict.Rd
View File

@ -69,7 +69,7 @@ ggplot_rsi_predict(
\item{minimum}{minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.}
\item{model}{the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See \emph{Details} for all valid options.}
\item{model}{the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using \code{glm(..., family = binomial)}, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See \emph{Details} for all valid options.}
\item{I_as_S}{a \link{logical} to indicate whether values \code{"I"} should be treated as \code{"S"} (will otherwise be treated as \code{"R"}). The default, \code{TRUE}, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section \emph{Interpretation of S, I and R} below.}