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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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10
man/as.mic.Rd
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@@ -33,7 +33,7 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati
This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
}
\details{
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2013-2022) and CLSI (2013-2022).
To interpret MIC values as SIR values, use \code{\link[=as.sir]{as.sir()}} on MIC values. It supports guidelines from EUCAST (2013-2022) and CLSI (2013-2022).
This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
@@ -82,7 +82,7 @@ mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
mic_data
is.mic(mic_data)
# this can also coerce combined MIC/RSI values:
# this can also coerce combined MIC/SIR values:
as.mic("<=0.002; S")
# mathematical processing treats MICs as numeric values
@@ -91,13 +91,13 @@ quantile(mic_data)
all(mic_data < 512)
# interpret MIC values
as.rsi(
as.sir(
x = as.mic(2),
mo = as.mo("Streptococcus pneumoniae"),
ab = "AMX",
guideline = "EUCAST"
)
as.rsi(
as.sir(
x = as.mic(c(0.01, 2, 4, 8)),
mo = as.mo("Streptococcus pneumoniae"),
ab = "AMX",
@@ -119,6 +119,6 @@ if (require("ggplot2")) {
}
}
\seealso{
\code{\link[=as.rsi]{as.rsi()}}
\code{\link[=as.sir]{as.sir()}}
}
\keyword{datasets}