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edit methodology of rsi

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dr. M.S. (Matthijs) Berends 2018-05-03 10:19:02 +02:00
parent c0fc82c794
commit 25b3346d9a
2 changed files with 12 additions and 41 deletions
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27
R/rsi_analysis.R
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@ -28,32 +28,17 @@
#' @param info calculate the amount of available isolates and print it, like \code{n = 423}
#' @param warning show a warning when the available amount of isolates is below \code{minimum}
#' @details Remember that you should filter your table to let it contain \strong{only first isolates}!
#'
#' To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:
#' \if{html}{
#' \cr \cr
#' To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:
#' \out{<div style="text-align: center">}\figure{mono_therapy.png}\out{</div>}
#' }
#' \if{latex}{
#' \deqn{p = \frac{\sum{ab1_S}}{\sum{ab1_{R|I|S}}}}
#' }
#' \cr
#' To calculate the probability (\emph{p}) of susceptibility of more antibiotics a combination therapy, we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). \cr
#' For two antibiotics:
#' \if{html}{
#' To calculate the probability (\emph{p}) of susceptibility of more antibiotics (i.e. combination therapy), we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). \cr
#' For two antibiotics:
#' \out{<div style="text-align: center">}\figure{combi_therapy_2.png}\out{</div>}
#' }
#' \if{latex}{
#' \deqn{p = \frac{\sum{ab1_S}\mid{ab2_S}}{\sum{ab1_{R|I|S},ab2_{R|I|S}}}}
#' }
#' \cr
#' For three antibiotics:
#' \if{html}{
#' \cr
#' For three antibiotics:
#' \out{<div style="text-align: center">}\figure{combi_therapy_3.png}\out{</div>}
#' }
#' \if{latex}{
#' \deqn{p = \frac{\sum{ab1_S}\mid{ab2_S}\mid{ab3_S}}{\sum{ab1_{R|I|S},ab2_{R|I|S},ab3_{R|I|S}}}}
#' }
#'
#' @keywords rsi antibiotics isolate isolates
#' @return Double or, when \code{as_percent = TRUE}, a character.
#' @rdname rsi

26
man/rsi.Rd
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@ -39,31 +39,17 @@ This functions can be used to calculate the (co-)resistance of isolates (i.e. pe
}
\details{
Remember that you should filter your table to let it contain \strong{only first isolates}!
To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:
\if{html}{
\cr \cr
To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:
\out{<div style="text-align: center">}\figure{mono_therapy.png}\out{</div>}
}
\if{latex}{
\deqn{p = \frac{\sum{ab1_S}}{\sum{ab1_{R|I|S}}}}
}
\cr
To calculate the probability (\emph{p}) of susceptibility of more antibiotics a combination therapy, we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). \cr
For two antibiotics:
\if{html}{
To calculate the probability (\emph{p}) of susceptibility of more antibiotics (i.e. combination therapy), we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). \cr
For two antibiotics:
\out{<div style="text-align: center">}\figure{combi_therapy_2.png}\out{</div>}
}
\if{latex}{
\deqn{p = \frac{\sum{ab1_S}\mid{ab2_S}}{\sum{ab1_{R|I|S},ab2_{R|I|S}}}}
}
\cr
For three antibiotics:
\if{html}{
\cr
For three antibiotics:
\out{<div style="text-align: center">}\figure{combi_therapy_3.png}\out{</div>}
}
\if{latex}{
\deqn{p = \frac{\sum{ab1_S}\mid{ab2_S}\mid{ab3_S}}{\sum{ab1_{R|I|S},ab2_{R|I|S},ab3_{R|I|S}}}}
}
}
\examples{
library(dplyr)