For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024, and for veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024.
- options(AMR_guideline = "CLSI")
options(AMR_guideline = "CLSI 2018")
options(AMR_guideline = "EUCAST 2020")
@@ -484,7 +485,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
mutate_if(is.mic, as.sir,
mo = "bacteria",
ab = "antibiotic",
- guideline = guideline
+ guideline = "guideline"
)
df_long %>%
mutate(across(
@@ -649,7 +650,162 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
#> column 'microorganism', EUCAST 2024...
#> 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.
-#> Error: object 'guideline' not found
+#>
+#> 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 2024...
+#> 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 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2024...
+#> 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 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2024...
+#> 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 2024...
+#> 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 2024...
+#> 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 2024...
+#> WARNING
+#> • No MIC breakpoints available for acetylspiramycin (ASP).
+#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
+#> CLSI 2024...
+#> WARNING
+#> • No DISK breakpoints available for acetylspiramycin (ASP).
+#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
+#> CLSI 2024...
+#> WARNING
+#> • No DISK breakpoints available for acetylspiramycin (ASP).
+#> Warning: There were 2 warnings in `mutate()`.
+#> The first warning was:
+#> 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 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), CLSI 2024...
+#> OK
+#> Warning: There were 2 warnings in `mutate()`.
+#> The first warning was:
+#> 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 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 2024...
+#> 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 2024...
+#> 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 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), EUCAST
+#> 2024...
+#> OK
+#> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin), EUCAST
+#> 2024...
+#> OK
+#> microorganism amoxicillin cipro tobra genta ERY
+#> 1 Escherichia coli 8 <NA> S S R
## Using base R ------------------------------------------------
@@ -681,20 +837,20 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
# return a 'logbook' about the results:
sir_interpretation_history()
-#> # A tibble: 29 × 17
+#> # A tibble: 65 × 17
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
-#> 1 2025-04-18 14:09:31 1 DISK ampicillin Strep pneu human 18
-#> 2 2025-04-18 14:09:31 1 DISK AMP Escherich… human 20
-#> 3 2025-04-18 14:09:31 1 DISK AMP Escherich… human 20
+#> 1 2025-04-18 15:20:04 1 DISK ampicillin Strep pneu human 18
+#> 2 2025-04-18 15:20:05 1 DISK AMP Escherich… human 20
+#> 3 2025-04-18 15:20:05 1 DISK AMP Escherich… human 20
#> 4 NA NA NA NA NA NA NA
-#> 5 2025-04-18 14:09:31 1 DISK GEN Escherich… human 18
-#> 6 2025-04-18 14:09:32 1 DISK TOB Escherich… human 16
-#> 7 2025-04-18 14:09:32 1 MIC AMX B_STRPT_P… human 2
-#> 8 2025-04-18 14:09:33 1 MIC AMX B_STRPT_P… human 0.01
-#> 9 2025-04-18 14:09:33 2 MIC AMX B_STRPT_P… human 2
-#> 10 2025-04-18 14:09:33 3 MIC AMX B_STRPT_P… human 4
-#> # ℹ 19 more rows
+#> 5 2025-04-18 15:20:05 1 DISK GEN Escherich… human 18
+#> 6 2025-04-18 15:20:05 1 DISK TOB Escherich… human 16
+#> 7 2025-04-18 15:20:06 1 MIC AMX B_STRPT_P… human 2
+#> 8 2025-04-18 15:20:06 1 MIC AMX B_STRPT_P… human 0.01
+#> 9 2025-04-18 15:20:06 2 MIC AMX B_STRPT_P… human 2
+#> 10 2025-04-18 15:20:06 3 MIC AMX B_STRPT_P… human 4
+#> # ℹ 55 more rows
#> # ℹ 10 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>
diff --git a/reference/atc_online.html b/reference/atc_online.html
index 751ba01b7..dc4e94340 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9242
+ 2.1.1.9243