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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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82
man/as.sir.Rd
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@@ -22,48 +22,86 @@ is.sir(x)
is_sir_eligible(x, threshold = 0.05)
\method{as.sir}{default}(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(), ...)
\method{as.sir}{default}(
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(),
...
)
\method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
\method{as.sir}{mic}(
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,
...
)
\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
\method{as.sir}{disk}(
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(),
...
)
\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
\method{as.sir}{data.frame}(
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)
}