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(v0.8.0.9027) adding susceptibility() and resistance()
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83
R/count.R
83
R/count.R
@ -23,20 +23,19 @@
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#'
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#' @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}.
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#'
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#' \code{count_R} and \code{count_IR} can be used to count resistant isolates, \code{count_S} and \code{count_SI} can be used to count susceptible isolates.\cr
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#' \code{count_resistant} should be used to count resistant isolates, \code{count_susceptible} should be used to count susceptible isolates.\cr
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#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.
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#' @inheritParams portion
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#' @inheritParams proportion
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#' @inheritSection as.rsi Interpretation of S, I and R
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#' @details These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance.
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#' @details These functions are meant to count isolates. Use the \code{\link{resistance}}/\code{\link{susceptibility}} functions to calculate microbial resistance/susceptibility.
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#'
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#' 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}.
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#'
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#' 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_S(...) + count_IR(...)}.
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#' 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(...)}.
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#'
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#' 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 amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
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#'
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#' The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
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#' @inheritSection portion Combination therapy
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#' @source Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
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#' @seealso \code{\link{portion}_*} to calculate microbial resistance and susceptibility.
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#' 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.
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#' @inheritSection proportion Combination therapy
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#' @seealso \code{\link{proportion}_*} to calculate microbial resistance and susceptibility.
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#' @return Integer
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#' @rdname count
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#' @name count
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@ -45,24 +44,28 @@
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#' @examples
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#' # example_isolates is a data set available in the AMR package.
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#' ?example_isolates
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#'
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#' count_resistant(example_isolates$AMX) # counts "R"
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#' count_susceptible(example_isolates$AMX) # counts "S" and "I"
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#' count_all(example_isolates$AMX) # counts "S", "I" and "R"
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#'
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#' # Count resistant isolates
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#' count_R(example_isolates$AMX)
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#' count_IR(example_isolates$AMX)
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#'
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#' # Or susceptible isolates
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#' # be more specific
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#' count_S(example_isolates$AMX)
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#' count_SI(example_isolates$AMX)
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#' count_I(example_isolates$AMX)
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#' count_IR(example_isolates$AMX)
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#' count_R(example_isolates$AMX)
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#'
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#' # Count all available isolates
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#' count_all(example_isolates$AMX)
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#' n_rsi(example_isolates$AMX)
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#'
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#' # Since n_rsi counts available isolates, you can
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#' # calculate back to count e.g. non-susceptible isolates.
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#' # This results in the same:
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#' count_SI(example_isolates$AMX)
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#' portion_SI(example_isolates$AMX) * n_rsi(example_isolates$AMX)
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#' # n_rsi() is an alias of count_all().
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#' # Since it counts all available isolates, you can
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#' # calculate back to count e.g. susceptible isolates.
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#' # These results are the same:
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#' count_susceptible(example_isolates$AMX)
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#' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
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#'
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#' library(dplyr)
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#' example_isolates %>%
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@ -76,19 +79,17 @@
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#'
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#' # Count co-resistance between amoxicillin/clav acid and gentamicin,
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#' # so we can see that combination therapy does a lot more than mono therapy.
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#' # Please mind that `portion_SI` calculates percentages right away instead.
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#' count_SI(example_isolates$AMC) # 1433
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#' count_all(example_isolates$AMC) # 1879
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#' # Please mind that `susceptibility()` calculates percentages right away instead.
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#' example_isolates %>% count_susceptible(AMC) # 1433
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#' example_isolates %>% count_all(AMC) # 1879
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#'
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#' count_SI(example_isolates$GEN) # 1399
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#' count_all(example_isolates$GEN) # 1855
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#' example_isolates %>% count_susceptible(GEN) # 1399
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#' example_isolates %>% count_all(GEN) # 1855
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#'
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#' with(example_isolates,
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#' count_SI(AMC, GEN)) # 1764
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#' with(example_isolates,
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#' n_rsi(AMC, GEN)) # 1936
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#'
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#' # Get portions S/I/R immediately of all rsi columns
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#' example_isolates %>% count_susceptible(AMC, GEN) # 1764
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#' example_isolates %>% count_all(AMC, GEN) # 1936
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#' # Get number of S+I vs. R immediately of selected columns
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#' example_isolates %>%
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#' select(AMX, CIP) %>%
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#' count_df(translate = FALSE)
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@ -99,6 +100,24 @@
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#' group_by(hospital_id) %>%
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#' count_df(translate = FALSE)
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#'
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count_resistant <- function(..., only_all_tested = FALSE) {
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rsi_calc(...,
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ab_result = "R",
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only_all_tested = only_all_tested,
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only_count = TRUE)
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}
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#' @rdname count
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#' @export
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count_susceptible <- function(..., only_all_tested = FALSE) {
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rsi_calc(...,
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ab_result = c("S", "I"),
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only_all_tested = only_all_tested,
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only_count = TRUE)
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}
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#' @rdname count
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#' @export
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count_R <- function(..., only_all_tested = FALSE) {
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rsi_calc(...,
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ab_result = "R",
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@ -109,6 +128,7 @@ count_R <- function(..., only_all_tested = FALSE) {
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#' @rdname count
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#' @export
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count_IR <- function(..., only_all_tested = FALSE) {
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warning("Using 'count_IR' is discouraged; use 'count_resistant()' instead to not consider \"I\" being resistant.", call. = FALSE)
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rsi_calc(...,
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ab_result = c("I", "R"),
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only_all_tested = only_all_tested,
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@ -136,6 +156,7 @@ count_SI <- function(..., only_all_tested = FALSE) {
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#' @rdname count
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#' @export
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count_S <- function(..., only_all_tested = FALSE) {
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warning("Using 'count_S' is discouraged; use 'count_susceptible()' instead to also consider \"I\" being susceptible.", call. = FALSE)
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rsi_calc(...,
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ab_result = "S",
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only_all_tested = only_all_tested,
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