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(v0.8.0.9029) cleanup

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dr. M.S. (Matthijs) Berends
2019-11-10 15:50:18 +01:00
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commit d22834c5b8
37 changed files with 351 additions and 348 deletions
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1
R/amr.R
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@ -52,6 +52,7 @@
#' University Medical Center Groningen \cr
#' Post Office Box 30001 \cr
#' 9700 RB Groningen
#' The Netherlands
#'
#' If you have found a bug, please file a new issue at: \cr
#' \url{https://gitlab.com/msberends/AMR/issues}

8
R/count.R
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@ -23,17 +23,17 @@
#'
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
#'
#' \code{count_resistant} should be used to count resistant isolates, \code{count_susceptible} should be used to count susceptible isolates.\cr
#' \code{count_resistant()} should be used to count resistant isolates, \code{count_susceptible()} should be used to count susceptible isolates.\cr
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.
#' @inheritParams proportion
#' @inheritSection as.rsi Interpretation of S, I and R
#' @details These functions are meant to count isolates. Use the \code{\link{resistance}}/\code{\link{susceptibility}} functions to calculate microbial resistance/susceptibility.
#'
#' The function \code{count_resistant} is equal to the function \code{count_R}. The function \code{count_susceptible} is equal to the function \code{count_SI}.
#' The function \code{count_resistant()} is equal to the function \code{count_R()}. The function \code{count_susceptible()} is equal to the function \code{count_SI()}.
#'
#' The function \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
#' The function \code{n_rsi()} is an alias of \code{count_all()}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
#'
#' The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the number of S's, I's and R's. The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
#' The function \code{count_df()} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}()}) and counts the number of S's, I's and R's. The function \code{rsi_df()} works exactly like \code{count_df()}, but adds the percentage of S, I and R.
#' @inheritSection proportion Combination therapy
#' @seealso \code{\link{proportion}_*} to calculate microbial resistance and susceptibility.
#' @return Integer

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R/mdro.R
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@ -21,7 +21,7 @@
#' Determine multidrug-resistant organisms (MDRO)
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.
#' @param info print progress
#' @inheritParams eucast_rules
@ -637,7 +637,7 @@ mdro <- function(x,
which(x$genus == "Staphylococcus" & x$species == "aureus"),
c(OXA, FOX),
"any")
trans_tbl2(paste("Table 1 -", italic("S. aureus")),
trans_tbl2(paste("Table 1 -", italic("Staphylococcus aureus")),
which(x$genus == "Staphylococcus" & x$species == "aureus"),
list(GEN,
RIF,

6
R/proportion.R
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@ -23,7 +23,7 @@
#'
#' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
#'
#' \code{resistance} should be used to calculate resistance, \code{susceptibility} should be used to calculate susceptibility.\cr
#' \code{resistance()} should be used to calculate resistance, \code{susceptibility()} should be used to calculate susceptibility.\cr
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.
#' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.
@ -35,13 +35,13 @@
#' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.
#' @inheritSection as.rsi Interpretation of S, I and R
#' @details
#' The function \code{resistance} is equal to the function \code{proportion_R}. The function \code{susceptibility} is equal to the function \code{proportion_SI}.
#' The function \code{resistance()} is equal to the function \code{proportion_R()}. The function \code{susceptibility()} is equal to the function \code{proportion_SI()}.
#'
#' \strong{Remember that you should filter your table to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link{first_isolate}} to determine them in your data set.
#'
#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. The function \code{susceptibility()} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can infuence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
#'
#' The function \code{proportion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the proportions R, I and S. The function \code{rsi_df} works exactly like \code{proportion_df}, but adds the number of isolates.
#' The function \code{proportion_df()} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}()}) and calculates the proportions R, I and S. The function \code{rsi_df()} works exactly like \code{proportion_df()}, but adds the number of isolates.
#' @section Combination therapy:
#' When using more than one variable for \code{...} (= combination therapy)), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how \code{susceptibility} works to calculate the \%SI:
#'

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R/rsi.R
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@ -46,7 +46,7 @@
#'
#' Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
#'
#' This AMR package honours this new insight. Use \code{\link{susceptibility}} (equal to \code{\link{proportion_SI}}) to determine antimicrobial susceptibility and \code{\link{count_susceptible}} (equal to \code{\link{count_SI}}) to count susceptible isolates.
#' This AMR package honours this new insight. Use \code{\link{susceptibility}()} (equal to \code{\link{proportion_SI}()}) to determine antimicrobial susceptibility and \code{\link{count_susceptible}()} (equal to \code{\link{count_SI}()}) to count susceptible isolates.
#' @return Ordered factor with new class \code{rsi}
#' @aliases RSI
#' @export