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(v1.0.0.9001) add uti to as.rsi()

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dr. M.S. (Matthijs) Berends
2020-02-20 17:21:01 +01:00
parent c6184a0fb8
commit bdb26f624f
12 changed files with 32 additions and 36 deletions
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27
R/rsi.R
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@ -87,10 +87,8 @@
#' as.rsi() # automatically determines urine isolates
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
#' mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
#'
#'
#'
#' # for single values
#' as.rsi(x = as.mic(2),
#' mo = as.mo("S. pneumoniae"),
@ -139,18 +137,25 @@ as.rsi.default <- function(x, ...) {
x
} else if (identical(levels(x), c("S", "I", "R"))) {
structure(x, class = c("rsi", "ordered", "factor"))
} else if (all_valid_mics(x) & !all(is.na(x))) {
as.rsi(as.mic(x), ab = deparse(substitute(x)), ...)
} else if (all_valid_disks(x) & !all(is.na(x))) {
#message("These values seem to be disk diffusion diameters and were treated as such.")
as.rsi(as.disk(x), ab = deparse(substitute(x)), ...)
} else if (identical(class(x), "integer") & all(x %in% c(1:3, NA))) {
} else if (inherits(x, "integer") & all(x %in% c(1:3, NA))) {
x[x == 1] <- "S"
x[x == 2] <- "I"
x[x == 3] <- "R"
structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
class = c("rsi", "ordered", "factor"))
} else {
ab <- deparse(substitute(x))
if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
if (!is.na(suppressWarnings(as.ab(ab)))) {
# check if they are actually MICs or disks now that the antibiotic name is valid
if (all_valid_mics(x)) {
as.rsi(as.mic(x), ab = ab, ...)
} else if (all_valid_disks(x)) {
as.rsi(as.disk(x), ab = ab, ...)
}
}
}
x <- x %>% unlist()
x.bak <- x
@ -632,9 +637,9 @@ plot.rsi <- function(x,
#' @importFrom graphics barplot axis par
#' @noRd
barplot.rsi <- function(height,
col = c("green3", "orange2", "red3"),
col = c("chartreuse4", "chartreuse3", "brown3"),
xlab = ifelse(beside, "Antimicrobial Interpretation", ""),
main = paste("Susceptibility Analysis of", deparse(substitute(height))),
main = paste("Antimicrobial resistance of", deparse(substitute(height))),
ylab = "Frequency",
beside = TRUE,
axes = beside,