P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 06:06:12 +01:00
Code Releases Activity

edit methodology of rsi

Browse Source
This commit is contained in:
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

27
R/rsi_analysis.R
View File

@ -28,32 +28,17 @@
#' @param info calculate the amount of available isolates and print it, like \code{n = 423} #' @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} #' @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}! #' @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}{ #' \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>} #' \out{<div style="text-align: center">}\figure{mono_therapy.png}\out{</div>}
#' } #' 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
#' \if{latex}{ #' For two antibiotics:
#' \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}{
#' \out{<div style="text-align: center">}\figure{combi_therapy_2.png}\out{</div>} #' \out{<div style="text-align: center">}\figure{combi_therapy_2.png}\out{</div>}
#' } #' \cr
#' \if{latex}{ #' For three antibiotics:
#' \deqn{p = \frac{\sum{ab1_S}\mid{ab2_S}}{\sum{ab1_{R|I|S},ab2_{R|I|S}}}}
#' }
#' \cr
#' For three antibiotics:
#' \if{html}{
#' \out{<div style="text-align: center">}\figure{combi_therapy_3.png}\out{</div>} #' \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 #' @keywords rsi antibiotics isolate isolates
#' @return Double or, when \code{as_percent = TRUE}, a character. #' @return Double or, when \code{as_percent = TRUE}, a character.
#' @rdname rsi #' @rdname rsi

26
man/rsi.Rd
View File

@ -39,31 +39,17 @@ This functions can be used to calculate the (co-)resistance of isolates (i.e. pe
} }
\details{ \details{
Remember that you should filter your table to let it contain \strong{only first isolates}! 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}{ \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>} \out{<div style="text-align: center">}\figure{mono_therapy.png}\out{</div>}
} 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
\if{latex}{ For two antibiotics:
\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}{
\out{<div style="text-align: center">}\figure{combi_therapy_2.png}\out{</div>} \out{<div style="text-align: center">}\figure{combi_therapy_2.png}\out{</div>}
} \cr
\if{latex}{ For three antibiotics:
\deqn{p = \frac{\sum{ab1_S}\mid{ab2_S}}{\sum{ab1_{R|I|S},ab2_{R|I|S}}}}
}
\cr
For three antibiotics:
\if{html}{
\out{<div style="text-align: center">}\figure{combi_therapy_3.png}\out{</div>} \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{ \examples{
library(dplyr) library(dplyr)