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styled, unit test fix
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209
R/proportion.R
209
R/proportion.R
@ -9,7 +9,7 @@
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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@ -40,7 +40,7 @@
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#' @inheritSection as.rsi Interpretation of R and S/I
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#' @details
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#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].
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#'
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#'
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#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set.
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#'
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#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [`count()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can influence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` argument).*
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@ -90,9 +90,9 @@
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#' @examples
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#' # example_isolates is a data set available in the AMR package.
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#' # run ?example_isolates for more info.
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#'
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#'
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#' # base R ------------------------------------------------------------
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#' resistance(example_isolates$AMX) # determines %R
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#' resistance(example_isolates$AMX) # determines %R
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#' susceptibility(example_isolates$AMX) # determines %S+I
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#'
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#' # be more specific
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@ -107,55 +107,65 @@
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' group_by(ward) %>%
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#' summarise(r = resistance(CIP),
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#' n = n_rsi(CIP)) # n_rsi works like n_distinct in dplyr, see ?n_rsi
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#'
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#' summarise(
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#' r = resistance(CIP),
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#' n = n_rsi(CIP)
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#' ) # n_rsi works like n_distinct in dplyr, see ?n_rsi
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#'
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#' example_isolates %>%
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#' group_by(ward) %>%
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#' summarise(R = resistance(CIP, as_percent = TRUE),
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#' SI = susceptibility(CIP, as_percent = TRUE),
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#' n1 = count_all(CIP), # the actual total; sum of all three
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#' n2 = n_rsi(CIP), # same - analogous to n_distinct
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#' total = n()) # NOT the number of tested isolates!
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#'
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#' summarise(
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#' R = resistance(CIP, as_percent = TRUE),
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#' SI = susceptibility(CIP, as_percent = TRUE),
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#' n1 = count_all(CIP), # the actual total; sum of all three
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#' n2 = n_rsi(CIP), # same - analogous to n_distinct
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#' total = n()
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#' ) # NOT the number of tested isolates!
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#'
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#' # Calculate 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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#' example_isolates %>% susceptibility(AMC) # %SI = 76.3%
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#' example_isolates %>% count_all(AMC) # n = 1879
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#'
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#' example_isolates %>% susceptibility(GEN) # %SI = 75.4%
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#' example_isolates %>% count_all(GEN) # n = 1855
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#'
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#' example_isolates %>% susceptibility(AMC) # %SI = 76.3%
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#' example_isolates %>% count_all(AMC) # n = 1879
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#'
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#' example_isolates %>% susceptibility(GEN) # %SI = 75.4%
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#' example_isolates %>% count_all(GEN) # n = 1855
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#'
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#' example_isolates %>% susceptibility(AMC, GEN) # %SI = 94.1%
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#' example_isolates %>% count_all(AMC, GEN) # n = 1939
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#'
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#'
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#' example_isolates %>% count_all(AMC, GEN) # n = 1939
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#'
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#'
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#' # See Details on how `only_all_tested` works. Example:
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#' example_isolates %>%
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#' summarise(numerator = count_susceptible(AMC, GEN),
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#' denominator = count_all(AMC, GEN),
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#' proportion = susceptibility(AMC, GEN))
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#'
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#' summarise(
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#' numerator = count_susceptible(AMC, GEN),
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#' denominator = count_all(AMC, GEN),
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#' proportion = susceptibility(AMC, GEN)
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#' )
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#'
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#' example_isolates %>%
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#' summarise(numerator = count_susceptible(AMC, GEN, only_all_tested = TRUE),
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#' denominator = count_all(AMC, GEN, only_all_tested = TRUE),
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#' proportion = susceptibility(AMC, GEN, only_all_tested = TRUE))
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#'
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#'
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#' summarise(
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#' numerator = count_susceptible(AMC, GEN, only_all_tested = TRUE),
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#' denominator = count_all(AMC, GEN, only_all_tested = TRUE),
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#' proportion = susceptibility(AMC, GEN, only_all_tested = TRUE)
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#' )
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#'
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#'
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#' example_isolates %>%
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#' group_by(ward) %>%
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#' summarise(cipro_p = susceptibility(CIP, as_percent = TRUE),
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#' cipro_n = count_all(CIP),
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#' genta_p = susceptibility(GEN, as_percent = TRUE),
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#' genta_n = count_all(GEN),
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#' combination_p = susceptibility(CIP, GEN, as_percent = TRUE),
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#' combination_n = count_all(CIP, GEN))
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#'
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#' summarise(
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#' cipro_p = susceptibility(CIP, as_percent = TRUE),
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#' cipro_n = count_all(CIP),
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#' genta_p = susceptibility(GEN, as_percent = TRUE),
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#' genta_n = count_all(GEN),
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#' combination_p = susceptibility(CIP, GEN, as_percent = TRUE),
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#' combination_n = count_all(CIP, GEN)
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#' )
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#'
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#' # Get proportions S/I/R immediately of all rsi columns
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#' example_isolates %>%
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#' select(AMX, CIP) %>%
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#' proportion_df(translate = FALSE)
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#'
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#'
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#' # It also supports grouping variables
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#' # (use rsi_df to also include the count)
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#' example_isolates %>%
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@ -170,12 +180,14 @@ resistance <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = "R",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = "R",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -186,12 +198,14 @@ susceptibility <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = c("S", "I"),
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = c("S", "I"),
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -202,12 +216,14 @@ proportion_R <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = "R",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = "R",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -218,12 +234,14 @@ proportion_IR <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = c("I", "R"),
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = c("I", "R"),
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -234,12 +252,14 @@ proportion_I <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = "I",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = "I",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -250,12 +270,14 @@ proportion_SI <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = c("S", "I"),
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = c("S", "I"),
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -266,12 +288,14 @@ proportion_S <- function(...,
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only_all_tested = FALSE) {
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tryCatch(
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rsi_calc(...,
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ab_result = "S",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE),
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error = function(e) stop_(e$message, call = -5))
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ab_result = "S",
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minimum = minimum,
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as_percent = as_percent,
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only_all_tested = only_all_tested,
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only_count = FALSE
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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#' @rdname proportion
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@ -284,14 +308,17 @@ proportion_df <- function(data,
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combine_SI = TRUE,
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combine_IR = FALSE) {
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tryCatch(
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rsi_calc_df(type = "proportion",
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data = data,
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translate_ab = translate_ab,
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language = language,
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minimum = minimum,
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as_percent = as_percent,
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combine_SI = combine_SI,
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combine_IR = combine_IR,
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combine_SI_missing = missing(combine_SI)),
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error = function(e) stop_(e$message, call = -5))
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rsi_calc_df(
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type = "proportion",
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data = data,
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translate_ab = translate_ab,
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language = language,
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minimum = minimum,
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as_percent = as_percent,
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combine_SI = combine_SI,
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combine_IR = combine_IR,
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combine_SI_missing = missing(combine_SI)
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),
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error = function(e) stop_(e$message, call = -5)
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)
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}
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