A vector specifying the antimicrobials containing SIR values to include in the antibiogram (see Examples). Will be evaluated using guess_ab_col(). This can be:
@@ -464,7 +464,8 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
bacteria = rep("Escherichia coli", 4),
antibiotic = c("amoxicillin", "cipro", "tobra", "genta"),
mics = as.mic(c(0.01, 1, 4, 8)),
-
disks = as.disk(c(6, 10, 14, 18))
+
disks = as.disk(c(6, 10, 14, 18)),
+
guideline = c("EUCAST 2021", "EUCAST 2022", "EUCAST 2023", "EUCAST 2024")
)
# \donttest{
@@ -483,7 +484,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
mutate_if(is.mic, as.sir,
mo = "bacteria",
ab = "antibiotic",
-
guideline = "CLSI"
+
guideline = guideline
)
df_long %>%
mutate(across(
@@ -648,166 +649,7 @@ 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.
-
#>
-
#> 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: `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.
-
#>
-
#> 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 CLSI 2024 MIC breakpoints available for acetylspiramycin (ASP).
-
#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
-
#> CLSI 2024...
-
#> WARNING
-
#> • No CLSI 2024 DISK breakpoints available for acetylspiramycin (ASP).
-
#> Interpreting disk diffusion zones: 'antibiotic' (ASP, acetylspiramycin),
-
#> CLSI 2024...
-
#> WARNING
-
#> • No CLSI 2024 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
+
#> Error: object 'guideline' not found
## Using base R ------------------------------------------------
@@ -839,20 +681,20 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
# return a 'logbook' about the results:
sir_interpretation_history()
-
#> # A tibble: 65 × 17
+
#> # A tibble: 29 × 17
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
-
#> 1 2025-04-14 07:56:09 1 DISK ampicillin Strep pneu human 18
-
#> 2 2025-04-14 07:56:09 1 DISK AMP Escherich… human 20
-
#> 3 2025-04-14 07:56:09 1 DISK AMP Escherich… human 20
+
#> 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
#> 4 NA NA NA NA NA NA NA
-
#> 5 2025-04-14 07:56:10 1 DISK GEN Escherich… human 18
-
#> 6 2025-04-14 07:56:10 1 DISK TOB Escherich… human 16
-
#> 7 2025-04-14 07:56:11 1 MIC AMX B_STRPT_P… human 2
-
#> 8 2025-04-14 07:56:11 1 MIC AMX B_STRPT_P… human 0.01
-
#> 9 2025-04-14 07:56:11 2 MIC AMX B_STRPT_P… human 2
-
#> 10 2025-04-14 07:56:11 3 MIC AMX B_STRPT_P… human 4
-
#> # ℹ 55 more rows
+
#> 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
#> # 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 d11ac283d..751ba01b7 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -1,5 +1,5 @@
-
Get ATC Properties from WHOCC Website — atc_online_property • AMR (for R)
+
Get ATC Properties from WHOCC Website — atc_online_property • AMR (for R)
Skip to contents
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9239
+
2.1.1.9242