Regarding choice of veterinary guidelines, these might be the best options to set before analysis:
@@ -484,7 +479,51 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
guideline = c("EUCAST 2021", "EUCAST 2022", "EUCAST 2023", "EUCAST 2024")
)
+
# most basic application:
+
as.sir(df_wide)
+
#> microorganism amoxicillin cipro tobra genta ERY
+
#> 1 Escherichia coli S I S S R
+
+
# return a 'logbook' about the results:
+
sir_interpretation_history()
+
#> # A tibble: 14 × 18
+
#> datetime index method ab_given mo_given host_given input_given
+
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
+
#> 1 2025-04-26 14:39:45 1 DISK ampicillin Strep pn… human 18
+
#> 2 2025-04-26 14:39:45 1 DISK AMP Escheric… human 20
+
#> 3 NA NA NA NA NA NA NA
+
#> 4 2025-04-26 14:39:46 1 DISK GEN Escheric… human 18
+
#> 5 2025-04-26 14:39:46 1 DISK TOB Escheric… human 16
+
#> 6 2025-04-26 14:39:47 1 MIC AMX B_STRPT_… human 2
+
#> 7 2025-04-26 14:39:47 1 MIC AMX B_STRPT_… human 0.01
+
#> 8 2025-04-26 14:39:47 2 MIC AMX B_STRPT_… human 2
+
#> 9 2025-04-26 14:39:47 3 MIC AMX B_STRPT_… human 4
+
#> 10 2025-04-26 14:39:47 4 MIC AMX B_STRPT_… human 8
+
#> 11 2025-04-26 14:39:53 1 MIC amoxicillin Escheric… human 8
+
#> 12 2025-04-26 14:39:53 1 MIC cipro Escheric… human 0.256
+
#> 13 2025-04-26 14:39:53 1 DISK tobra Escheric… human 16
+
#> 14 2025-04-26 14:39:54 1 DISK genta Escheric… human 18
+
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
+
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
+
#> # breakpoint_S_R <chr>, site <chr>
+
# \donttest{
+
# using parallel computing, which is available in base R:
+
as.sir(df_wide, parallel = TRUE, info = TRUE)
+
#> ℹ Returning previously coerced values for various antimicrobials. Run
+
#> ab_reset_session() to reset this. This note will be shown once per
+
#> session.
+
#>
+
#> Running SIR interpretation in parallel mode on five columns, using 3 out of
+
#> 4 cores...
+
#> Done.
+
#>
+
#> ℹ Run sir_interpretation_history() to retrieve a logbook with all the
+
#> details of the breakpoint interpretations.
+
#> microorganism amoxicillin cipro tobra genta ERY
+
#> 1 Escherichia coli S I S S R
+
+
## Using dplyr -------------------------------------------------
if (require("dplyr")) {
# approaches that all work without additional arguments:
@@ -589,239 +628,46 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
df_wide %>%
mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE)
}
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on
-
#> column 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin) based on
-
#> column 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on
-
#> column 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column
-
#> 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on
-
#> column 'microorganism', EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
-
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
-
#> 'bacteria', EUCAST 2021, EUCAST 2022, EUCAST 2023, and EUCAST 2024...
-
#> NOTE
-
#> • There were multiple notes. Print or View sir_interpretation_history() to examine them, or use as.sir(..., verbose = TRUE) next time to directly print them here.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
-
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
-
#> 'bacteria', CLSI 2025...
-
#> OK
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2025...
-
#> OK
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `cipro = (function (x, ...) ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2025...
-
#> OK
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> ℹ Assuming breakpoint_type = "animal", since host is set.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
-
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
-
#> 'bacteria', CLSI 2025...
-
#> OK
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `mics = (function (x, ...) ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> ℹ Assuming breakpoint_type = "animal", since host is set.
-
#>
-
#> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),
-
#> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column
-
#> 'bacteria', CLSI 2025...
-
#> OK
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> ℹ Assuming breakpoint_type = "animal", since host is set.
-
#>
-
#>
#> Interpreting MIC values: 'antibiotic' (ASP, acetylspiramycin), CLSI 2025...
-
#> WARNING
-
#> • No MIC breakpoints available for acetylspiramycin (ASP).
#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
#> CLSI 2025...
-
#> WARNING
-
#> • No DISK breakpoints available for acetylspiramycin (ASP).
#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
#> CLSI 2025...
-
#> WARNING
-
#> • No DISK breakpoints available for acetylspiramycin (ASP).
-
#> Warning: There were 2 warnings in `mutate()`.
-
#> The first warning was:
+
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `cipro = (function (x, ...) ...`.
#> Caused by warning:
-
#> ! The following animal host(s) could not be coerced: "animal_species"
-
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> ℹ Assuming breakpoint_type = "animal", since host is set.
-
#>
-
#>
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2025...
-
#> OK
-
#> Warning: There were 2 warnings in `mutate()`.
-
#> The first warning was:
+
#> ! Some MICs were converted to the nearest higher log2 level, following the
+
#> CLSI interpretation guideline.
+
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
-
#> ! The following animal host(s) could not be coerced: "animal_species"
-
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
-
#> ℹ Returning previously coerced values for "E. coli". Run
-
#> mo_reset_session() to reset this. This note will be shown once per
-
#> session for this input.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,
-
#> nitrofurantoin), EUCAST 2025...
-
#> OK
-
#> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract
-
#> infection.
-
#> Use as.sir(uti = FALSE) to prevent this.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,
-
#> nitrofurantoin), EUCAST 2025...
-
#> OK
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), EUCAST 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), EUCAST
-
#> 2025...
-
#> OK
-
#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), EUCAST
-
#> 2025...
-
#> OK
+
#> ! Some MICs were converted to the nearest higher log2 level, following the
+
#> CLSI interpretation guideline.
#> microorganism amoxicillin cipro tobra genta ERY
#> 1 Escherichia coli 8 <NA> S S R
@@ -829,52 +675,33 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
## Using base R ------------------------------------------------
as.sir(df_wide)
-
#>
-
#> ℹ Running SIR interpretation in sequential mode. Consider setting parallel
-
#> = TRUE to speed up processing on multiple cores.
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: column 'amoxicillin' (AMX), EUCAST 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting MIC values: column 'cipro' (CIP, ciprofloxacin), EUCAST
-
#> 2025...
-
#> NOTE
-
#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
-
#> Interpreting disk diffusion zones: column 'tobra' (TOB, tobramycin), EUCAST
-
#> 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Interpreting disk diffusion zones: column 'genta' (GEN, gentamicin), EUCAST
-
#> 2025...
-
#> NOTE
-
#> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.
-
#> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...
-
#> OK
#> microorganism amoxicillin cipro tobra genta ERY
#> 1 Escherichia coli S I S S R
# return a 'logbook' about the results:
sir_interpretation_history()
-
#> # A tibble: 54 × 18
-
#> datetime index method ab_given mo_given host_given input_given
-
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
-
#> 1 2025-04-26 13:53:13 1 MIC amoxicillin Escheric… human 8
-
#> 2 2025-04-26 13:53:14 1 MIC cipro Escheric… human 0.256
-
#> 3 2025-04-26 13:53:14 1 MIC amoxicillin Escheric… human 8
-
#> 4 2025-04-26 13:53:14 1 MIC cipro Escheric… human 0.256
-
#> 5 2025-04-26 13:53:14 1 DISK tobra Escheric… human 16
-
#> 6 2025-04-26 13:53:15 1 DISK genta Escheric… human 18
-
#> 7 2025-04-26 13:53:15 1 MIC amoxicillin Escheric… human 8
-
#> 8 2025-04-26 13:53:15 1 MIC cipro Escheric… human 0.256
-
#> 9 2025-04-26 13:53:15 1 MIC amoxicillin Escheric… human 8
-
#> 10 2025-04-26 13:53:16 1 MIC cipro Escheric… human 0.256
-
#> # ℹ 44 more rows
+
#> # A tibble: 114 × 18
+
#> datetime index method ab_given mo_given host_given input_given
+
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
+
#> 1 2025-04-26 14:39:45 1 DISK ampicillin Strep pneu human 18
+
#> 2 2025-04-26 14:39:45 1 DISK AMP Escherich… human 20
+
#> 3 NA NA NA NA NA NA NA
+
#> 4 2025-04-26 14:39:46 1 DISK GEN Escherich… human 18
+
#> 5 2025-04-26 14:39:46 1 DISK TOB Escherich… human 16
+
#> 6 2025-04-26 14:39:47 1 MIC AMX B_STRPT_P… human 2
+
#> 7 2025-04-26 14:39:47 1 MIC AMX B_STRPT_P… human 0.01
+
#> 8 2025-04-26 14:39:47 2 MIC AMX B_STRPT_P… human 2
+
#> 9 2025-04-26 14:39:47 3 MIC AMX B_STRPT_P… human 4
+
#> 10 2025-04-26 14:39:47 4 MIC AMX B_STRPT_P… human 8
+
#> # ℹ 104 more rows
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
-
#> # breakpoint_S_R <chr>, site <lgl>
+
#> # breakpoint_S_R <chr>, site <chr>
+
+
# using parallel computing, which is available in base R
+
as.sir(df_wide, parallel = TRUE)
+
#> microorganism amoxicillin cipro tobra genta ERY
+
#> 1 Escherichia coli S I S S R
# for single values
as.sir(
@@ -883,12 +710,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
ab = "AMP",
guideline = "EUCAST"
)
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2025...
-
#> Error in rbindlist(l, use.names, fill, idcol, ignore.attr): Class attribute on column 5 of item 2 does not match with column 5 of item 1. You can deactivate this safety-check by using ignore.attr=TRUE
+
#> Class 'sir'
+
#> [1] R
as.sir(
x = as.disk(18),
@@ -896,12 +719,6 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST"
)
-
#>
-
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-
#> all the details of the breakpoint interpretations.
-
#>
-
#> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2025...
-
#> OK
#> Class 'sir'
#> [1] R
@@ -943,9 +760,6 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
# example_isolates %>%
# mutate(across(where(is_sir_eligible), as.sir))
}
-
#>
-
#> ℹ Running SIR interpretation in sequential mode. Consider setting parallel
-
#> = TRUE to speed up processing on multiple cores.
#> # A tibble: 2,000 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
diff --git a/reference/atc_online.html b/reference/atc_online.html
index 7aa8c8da5..caafb37c6 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9253
+
2.1.1.9255