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(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
This commit is contained in:
@ -72,12 +72,15 @@ Other contributors:
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\item Dmytro Mykhailenko [contributor]
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\item Eric H. L. C. M. Hazenberg [contributor]
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\item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
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\item Jane Hawkey (\href{https://orcid.org/0000-0001-9661-5293}{ORCID}) [contributor]
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\item Jason Stull (\href{https://orcid.org/0000-0002-9028-8153}{ORCID}) [contributor]
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\item Javier Sanchez (\href{https://orcid.org/0000-0003-2605-8094}{ORCID}) [contributor]
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\item Jonas Salm [contributor]
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\item Judith M. Fonville [contributor]
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\item Kathryn Holt (\href{https://orcid.org/0000-0003-3949-2471}{ORCID}) [contributor]
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\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
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\item Matthew Saab [contributor]
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\item Natacha Couto (\href{https://orcid.org/0000-0002-9152-5464}{ORCID}) [contributor]
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\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
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\item Rogier P. Schade [contributor]
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\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
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@ -30,6 +30,7 @@
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\alias{quinolones}
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\alias{rifamycins}
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\alias{streptogramins}
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\alias{sulfonamides}
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\alias{tetracyclines}
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\alias{trimethoprims}
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\alias{ureidopenicillins}
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@ -107,6 +108,8 @@ rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
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streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
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sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)
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tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
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return_all = TRUE, ...)
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@ -203,6 +206,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
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\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
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\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)
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\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
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\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13)
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\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC)
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\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
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\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)
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@ -33,7 +33,7 @@ is.sir(x)
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is_sir_eligible(x, threshold = 0.05)
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\method{as.sir}{default}(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
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NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", ...)
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NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = TRUE, ...)
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\method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
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guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
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@ -44,7 +44,7 @@ is_sir_eligible(x, threshold = 0.05)
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FALSE), include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
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verbose = FALSE, conserve_capped_values = NULL, ...)
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verbose = FALSE, info = TRUE, conserve_capped_values = NULL, ...)
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\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
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guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
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@ -54,7 +54,7 @@ is_sir_eligible(x, threshold = 0.05)
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FALSE), include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
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verbose = FALSE, ...)
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verbose = FALSE, info = TRUE, ...)
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\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
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guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
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@ -65,7 +65,7 @@ is_sir_eligible(x, threshold = 0.05)
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FALSE), include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
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verbose = FALSE, conserve_capped_values = NULL)
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verbose = FALSE, info = TRUE, conserve_capped_values = NULL)
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sir_interpretation_history(clean = FALSE)
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}
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@ -78,6 +78,8 @@ sir_interpretation_history(clean = FALSE)
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\item{S, I, R, NI, SDD}{a case-independent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters and whitespaces are removed from the input.}
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\item{info}{a \link{logical} to print information about the process}
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\item{mo}{a vector (or column name) with \link{character}s that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
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\item{ab}{a vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
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@ -51,7 +51,7 @@ df
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#> 1 Escherichia coli R S S
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#> 2 Klebsiella pneumoniae R S S
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eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
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eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
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#> mo TZP ampi cipro
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#> 1 Escherichia coli R R S
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#> 2 Klebsiella pneumoniae R R S
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@ -65,7 +65,7 @@ There is one exception in columns used for the rules: all column names of the \l
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
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TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
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eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
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eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
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#> mo TZP ampi cipro
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#> 1 Escherichia coli R S S
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#> 2 Klebsiella pneumoniae R R S
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@ -86,7 +86,7 @@ x
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#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
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}\if{html}{\out{</div>}}
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These 34 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
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These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
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\itemize{
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\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, 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)
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\item aminopenicillins\cr(amoxicillin and ampicillin)
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@ -118,6 +118,7 @@ These 34 antimicrobial groups are allowed in the rules (case-insensitive) and ca
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\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
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\item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
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\item streptogramins\cr(pristinamycin and quinupristin/dalfopristin)
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\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)
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\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline)
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\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)
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\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)
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@ -138,6 +139,7 @@ eucast_rules(example_isolates,
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rules = "custom",
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custom_rules = x,
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info = FALSE,
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overwrite = TRUE,
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verbose = TRUE
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)
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@ -3,9 +3,9 @@
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\docType{data}
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\name{microorganisms}
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\alias{microorganisms}
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\title{Data Set with 78 678 Taxonomic Records of Microorganisms}
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\title{Data Set with 78 679 Taxonomic Records of Microorganisms}
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\format{
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A \link[tibble:tibble]{tibble} with 78 678 observations and 26 variables:
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A \link[tibble:tibble]{tibble} with 78 679 observations and 26 variables:
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\itemize{
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\item \code{mo}\cr ID of microorganism as used by this package. \emph{\strong{This is a unique identifier.}}
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\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. \emph{\strong{This is a unique identifier.}}
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@ -14,7 +14,7 @@ A \link[tibble:tibble]{tibble} with 78 678 observations and 26 variables:
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\item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}
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\item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.
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\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3\% of all ~39 000 bacteria in the data set contain an oxygen tolerance.
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\item \code{source}\cr Either "GBIF", "LPSN", "MycoBank", or "manually added" (see \emph{Source})
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\item \code{source}\cr Either "GBIF", "LPSN", "Manually added", "MycoBank", or "manually added" (see \emph{Source})
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\item \code{lpsn}\cr Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, \emph{Acetobacter ascendens} has LPSN Record number 7864 and 11011. Only the first is available in the \code{microorganisms} data set. \emph{\strong{This is a unique identifier}}, though available for only ~33 000 records.
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\item \code{lpsn_parent}\cr LPSN identifier of the parent taxon
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\item \code{lpsn_renamed_to}\cr LPSN identifier of the currently valid taxon
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@ -80,7 +80,7 @@ Included taxonomic data from \href{https://lpsn.dsmz.de}{LPSN}, \href{https://ww
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For convenience, some entries were added manually:
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\itemize{
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\item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H
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\item 36 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
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\item 37 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
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\item 1 entry of \emph{Blastocystis} (\emph{B. hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
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\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
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\item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
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@ -3,9 +3,9 @@
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\docType{data}
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\name{microorganisms.groups}
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\alias{microorganisms.groups}
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\title{Data Set with 521 Microorganisms In Species Groups}
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\title{Data Set with 534 Microorganisms In Species Groups}
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\format{
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A \link[tibble:tibble]{tibble} with 521 observations and 4 variables:
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A \link[tibble:tibble]{tibble} with 534 observations and 4 variables:
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\itemize{
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\item \code{mo_group}\cr ID of the species group / microbiological complex
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\item \code{mo}\cr ID of the microorganism belonging in the species group / microbiological complex
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