Added function n_rsi

man/EUCAST.Rd

@@ -50,6 +50,7 @@ table with edited variables of antibiotics.
 Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
 }
 \examples{
+a <- EUCAST_rules(septic_patients)
 a <- data.frame(bactid = c("STAAUR",  # Staphylococcus aureus
                            "ENCFAE",  # Enterococcus faecalis
                            "ESCCOL",  # Escherichia coli

man/rsi.Rd

@@ -2,49 +2,106 @@
 % Please edit documentation in R/rsi_analysis.R
 \name{rsi}
 \alias{rsi}
+\alias{rsi_df}
+\alias{n_rsi}
 \title{Resistance of isolates}
 \usage{
-rsi(ab1, ab2 = NA, interpretation = "IR", minimum = 30, percent = FALSE,
-  info = FALSE, warning = FALSE)
+rsi(ab1, ab2 = NA, interpretation = "IR", minimum = 30,
+  as_percent = FALSE, info = FALSE, warning = TRUE)
+
+rsi_df(tbl, ab, interpretation = "IR", minimum = 30, as_percent = FALSE,
+  info = TRUE, warning = TRUE)
+
+n_rsi(ab1, ab2 = NA)
 }
 \arguments{
-\item{ab1, ab2}{list with interpretations of an antibiotic}
+\item{ab1, ab2}{vector of antibiotic interpretations, they will be transformed internally with \code{\link{as.rsi}}}
 
 \item{interpretation}{antimicrobial interpretation of which the portion must be calculated. Valid values are \code{"S"}, \code{"SI"}, \code{"I"}, \code{"IR"} or \code{"R"}.}
 
 \item{minimum}{minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA} with a warning (when \code{warning = TRUE}).}
 
-\item{percent}{return output as percent (text), will else (at default) be a double}
+\item{as_percent}{return output as percent (text), will else (at default) be a double}
 
 \item{info}{calculate the amount of available isolates and print it, like \code{n = 423}}
 
 \item{warning}{show a warning when the available amount of isolates is below \code{minimum}}
+
+\item{tbl}{\code{data.frame} containing columns with antibiotic interpretations.}
+
+\item{ab}{character vector with 1, 2 or 3 antibiotics that occur as column names in \code{tbl}, like \code{ab = c("amox", "amcl")}}
 }
 \value{
-Double or, when \code{percent = TRUE}, a character.
+Double or, when \code{as_percent = TRUE}, a character.
 }
 \description{
-This function can be used in \code{dplyr}s \code{\link[dplyr]{summarise}}, see \emph{Examples}. Calculate the percentage S, SI, I, IR or R of a vector of isolates.
+This functions can be used to calculate the (co-)resistance of isolates (i.e. percentage S, SI, I, IR or R [of a vector] of isolates). The functions \code{rsi} and \code{n_rsi} can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
 }
 \details{
-This function uses the \code{\link{rsi_df}} function internally.
+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}{
+  \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}{
+  \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}{
+  \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)
+
+septic_patients \%>\%
+  group_by(hospital_id) \%>\%
+  summarise(cipro_susceptibility = rsi(cipr, interpretation = "S"),
+            n = n_rsi(cipr)) # n_rsi works like n_distinct in dplyr
+
+septic_patients \%>\%
+  group_by(hospital_id) \%>\%
+  summarise(cipro_S = rsi(cipr, interpretation = "S",
+                          as_percent = TRUE, warning = FALSE),
+            cipro_n = n_rsi(cipr),
+            genta_S = rsi(gent, interpretation = "S",
+                          as_percent = TRUE, warning = FALSE),
+            genta_n = n_rsi(gent),
+            combination_S = rsi(cipr, gent, interpretation = "S",
+                                as_percent = TRUE, warning = FALSE),
+            combination_n = n_rsi(cipr, gent))
+
+# calculate resistance
+rsi(septic_patients$amox)
+# or susceptibility
+rsi(septic_patients$amox, interpretation = "S")
+
+# calculate co-resistance between amoxicillin/clav acid and gentamicin,
+# so we can review that combination therapy does a lot more than mono therapy:
+septic_patients \%>\% rsi_df(ab = "amcl", interpretation = "S") # = 67.8\%
+septic_patients \%>\% rsi_df(ab = "gent", interpretation = "S") # = 69.1\%
+septic_patients \%>\% rsi_df(ab = c("amcl", "gent"), interpretation = "S") # = 90.6\%
+
 \dontrun{
-tbl \%>\%
-  group_by(hospital) \%>\%
-  summarise(cipr = rsi(cipr))
-
-tbl \%>\%
-  group_by(year, hospital) \%>\%
-  summarise(
-    isolates = n(),
-    cipro = rsi(cipr \%>\% as.rsi(), percent = TRUE),
-    amoxi = rsi(amox \%>\% as.rsi(), percent = TRUE))
-
-rsi(as.rsi(isolates$amox))
-
-rsi(as.rsi(isolates$amcl), interpretation = "S")
+# calculate current empiric combination therapy of Helicobacter gastritis:
+my_table \%>\%
+  filter(first_isolate == TRUE,
+         genus == "Helicobacter") \%>\%
+  rsi_df(ab = c("amox", "metr")) # amoxicillin with metronidazole
 }
 }
 \keyword{antibiotics}

man/rsi_df.Rd

@@ -1,54 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/rsi_analysis.R
-\name{rsi_df}
-\alias{rsi_df}
-\title{Resistance of isolates in data.frame}
-\usage{
-rsi_df(tbl, ab, interpretation = "IR", minimum = 30, percent = FALSE,
-  info = TRUE, warning = TRUE)
-}
-\arguments{
-\item{tbl}{\code{data.frame} containing columns with antibiotic interpretations.}
-
-\item{ab}{character vector with 1, 2 or 3 antibiotics that occur as column names in \code{tbl}, like \code{ab = c("amox", "amcl")}}
-
-\item{interpretation}{antimicrobial interpretation of which the portion must be calculated. Valid values are \code{"S"}, \code{"SI"}, \code{"I"}, \code{"IR"} or \code{"R"}.}
-
-\item{minimum}{minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA} with a warning (when \code{warning = TRUE}).}
-
-\item{percent}{return output as percent (text), will else (at default) be a double}
-
-\item{info}{calculate the amount of available isolates and print it, like \code{n = 423}}
-
-\item{warning}{show a warning when the available amount of isolates is below \code{minimum}}
-}
-\value{
-Double or, when \code{percent = TRUE}, a character.
-}
-\description{
-\strong{NOTE: use \code{\link{rsi}} in dplyr functions like \code{\link[dplyr]{summarise}}.} \cr Calculate the percentage of S, SI, I, IR or R of a \code{data.frame} containing isolates.
-}
-\details{
-Remember that you should filter your table to let it contain \strong{only first isolates}!
-}
-\examples{
-\dontrun{
-rsi_df(tbl_with_bloodcultures, 'amcl')
-
-rsi_df(tbl_with_bloodcultures, c('amcl', 'gent'), interpretation = 'IR')
-
-library(dplyr)
-# calculate current empiric therapy of Helicobacter gastritis:
-my_table \%>\%
-  filter(first_isolate == TRUE,
-         genus == "Helicobacter") \%>\%
-  rsi_df(ab = c("amox", "metr"))
-}
-}
-\seealso{
-\code{\link{rsi}} for the function that can be used with \code{\link[dplyr]{summarise}} directly.
-}
-\keyword{antibiotics}
-\keyword{isolate}
-\keyword{isolates}
-\keyword{rsi}