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reference/as.sir.md
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@@ -2,13 +2,16 @@
Clean up existing SIR values, or interpret minimum inhibitory
concentration (MIC) values and disk diffusion diameters according to
EUCAST or CLSI. \[as.sir()\] transforms the input to a new class
\[\`sir\`\], which is an ordered \[factor\] containing the levels \`S\`,
\`SDD\`, \`I\`, \`R\`, \`NI\`.
EUCAST or CLSI. `as.sir()` transforms the input to a new class `sir`,
which is an ordered
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) containing the
levels `S`, `SDD`, `I`, `R`, `NI`.
Breakpoints are currently implemented from EUCAST \`r
min(as.integer(gsub("\[^0-9\]", "", subset(AMR::clinical_breakpoints,
guideline
Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI
2011-2026, see *Details*. All breakpoints used for interpretation are
available in our
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set.
## Usage
@@ -22,86 +25,93 @@ is.sir(x)
is_sir_eligible(x, threshold = 0.05)
# Default S3 method
as.sir(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
WT = "^(WT|6)+$", NWT = "^(NWT|7)+$", NS = "^(NS|8)+$",
info = interactive(), ...)
as.sir(
x,
S = "^(S|U|1)+$",
I = "^(I|2)+$",
R = "^(R|3)+$",
NI = "^(N|NI|V|4)+$",
SDD = "^(SDD|D|H|5)+$",
WT = "^(WT|6)+$",
NWT = "^(NWT|7)+$",
NS = "^(NS|8)+$",
info = interactive(),
...
)
# S3 method for class 'mic'
as.sir(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
as.sir(
x,
mo = NULL,
ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"),
uti = NULL,
capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
as_wt_nwt = identical(breakpoint_type, "ECOFF"),
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
FALSE),
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
conserve_capped_values = NULL, ...)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
host = NULL,
language = get_AMR_locale(),
verbose = FALSE,
info = interactive(),
conserve_capped_values = NULL,
...
)
# S3 method for class 'disk'
as.sir(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
as.sir(
x,
mo = NULL,
ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"),
uti = NULL,
as_wt_nwt = identical(breakpoint_type, "ECOFF"),
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
FALSE),
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
...)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
host = NULL,
language = get_AMR_locale(),
verbose = FALSE,
info = interactive(),
...
)
# S3 method for class 'data.frame'
as.sir(x, ..., col_mo = NULL,
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
as.sir(
x,
...,
col_mo = NULL,
guideline = getOption("AMR_guideline", "EUCAST"),
uti = NULL,
capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
as_wt_nwt = identical(breakpoint_type, "ECOFF"),
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
FALSE),
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
parallel = FALSE, conserve_capped_values = NULL)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
host = NULL,
language = get_AMR_locale(),
verbose = FALSE,
info = interactive(),
parallel = FALSE,
conserve_capped_values = NULL
)
sir_interpretation_history(clean = FALSE)
```
## Source
For interpretations of minimum inhibitory concentration (MIC) values and
disk diffusion diameters:
- **CLSI M39: Analysis and Presentation of Cumulative Antimicrobial
Susceptibility Test Data**, 2011-2026, *Clinical and Laboratory
Standards Institute* (CLSI).
<https://clsi.org/standards/products/microbiology/documents/m39/>.
- **CLSI M100: Performance Standard for Antimicrobial Susceptibility
Testing**, 2011-2026, *Clinical and Laboratory Standards Institute*
(CLSI).
<https://clsi.org/standards/products/microbiology/documents/m100/>.
- **CLSI VET01: Performance Standards for Antimicrobial Disk and
Dilution Susceptibility Tests for Bacteria Isolated From Animals**,
2019-2026, *Clinical and Laboratory Standards Institute* (CLSI).
<https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
- **EUCAST Breakpoint tables for interpretation of MICs and zone
diameters**, 2011-2026, *European Committee on Antimicrobial
Susceptibility Testing* (EUCAST).
<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
- **WHONET** as a source for machine-reading the clinical breakpoints
([read more
here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)),
1989-2026, *WHO Collaborating Centre for Surveillance of Antimicrobial
Resistance*. <https://whonet.org/>.
## Arguments
- x:
@@ -364,7 +374,8 @@ disk diffusion diameters:
## Value
Ordered \[factor\] with new class \`sir\`
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with new
class `sir`
## Details
@@ -577,6 +588,37 @@ links](https://amr-for-r.org/articles/datasets.html), or explore the
actual files in [our GitHub
repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
## References
For interpretations of minimum inhibitory concentration (MIC) values and
disk diffusion diameters:
- **CLSI M39: Analysis and Presentation of Cumulative Antimicrobial
Susceptibility Test Data**, 2011-2026, *Clinical and Laboratory
Standards Institute* (CLSI).
<https://clsi.org/standards/products/microbiology/documents/m39/>.
- **CLSI M100: Performance Standard for Antimicrobial Susceptibility
Testing**, 2011-2026, *Clinical and Laboratory Standards Institute*
(CLSI).
<https://clsi.org/standards/products/microbiology/documents/m100/>.
- **CLSI VET01: Performance Standards for Antimicrobial Disk and
Dilution Susceptibility Tests for Bacteria Isolated From Animals**,
2019-2026, *Clinical and Laboratory Standards Institute* (CLSI).
<https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
- **EUCAST Breakpoint tables for interpretation of MICs and zone
diameters**, 2011-2026, *European Committee on Antimicrobial
Susceptibility Testing* (EUCAST).
<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
- **WHONET** as a source for machine-reading the clinical breakpoints
([read more
here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)),
1989-2026, *WHO Collaborating Centre for Surveillance of Antimicrobial
Resistance*. <https://whonet.org/>.
## See also
[`as.mic()`](https://amr-for-r.org/reference/as.mic.md),
@@ -663,10 +705,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-05-02 13:02:42 1 MIC amoxicillin Escherich… human 8
#> 2 2026-05-02 13:02:42 1 MIC cipro Escherich… human 0.256
#> 3 2026-05-02 13:02:42 1 DISK tobra Escherich… human 16
#> 4 2026-05-02 13:02:43 1 DISK genta Escherich… human 18
#> 1 2026-06-23 17:55:31 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-23 17:55:31 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-23 17:55:32 1 DISK tobra Escherich… human 16
#> 4 2026-06-23 17:55:32 1 DISK genta Escherich… 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>