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(v1.6.0.9021) join functions update

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dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
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12
man/as.mic.Rd
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@ -11,12 +11,12 @@ as.mic(x, na.rm = FALSE)
is.mic(x)
}
\arguments{
\item{x}{character or numeric vector}
\item{x}{a \link{character} or \link{numeric} vector}
\item{na.rm}{a logical indicating whether missing values should be removed}
\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
}
\value{
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a numeric value.
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
}
\description{
This ransforms 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.
@ -24,7 +24,7 @@ This ransforms vectors to a new class \code{\link{mic}}, which treats the input
\details{
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST and CLSI.
This class for MIC values is a quite a special data type: formally it is an ordered factor with valid MIC values as factor levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:\preformatted{x <- random_mic(10)
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:\preformatted{x <- random_mic(10)
x
#> Class <mic>
#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
@ -39,7 +39,7 @@ median(x)
#> [1] 26
}
This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using numeric values in data analysis, e.g.:\preformatted{x[x > 4]
This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:\preformatted{x[x > 4]
#> Class <mic>
#> [1] 16 8 8 64 >=128 32 32 16
@ -76,7 +76,7 @@ is.mic(mic_data)
# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; S") # will return <=0.002
# mathematical processing treats MICs as numeric values
# mathematical processing treats MICs as [numeric] values
fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)