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(v1.8.0.9004) MIC printing in tibbles

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dr. M.S. (Matthijs) Berends
2022-03-03 21:11:02 +01:00
parent dedbe92322
commit ad82bb4ce0
61 changed files with 85 additions and 79 deletions
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8
R/mic.R
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@ -37,8 +37,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
function(x) paste0(x, sort(c(1:9, 1.5)))))),
c(t(vapply(FUN.VALUE = character(45), ops,
function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
c(t(vapply(FUN.VALUE = character(16), ops,
function(x) paste0(x, sort(c(2 ^ c(7:11), 80 * c(2:12))))))))
c(t(vapply(FUN.VALUE = character(17), ops,
function(x) paste0(x, sort(c(2 ^ c(7:11), 192, 80 * c(2:12))))))))
#' Transform Input to Minimum Inhibitory Concentrations (MIC)
#'
@ -247,7 +247,9 @@ pillar_shaft.mic <- function(x, ...) {
out <- pasted
out[is.na(x)] <- font_na(NA)
out <- gsub("(<|=|>)", font_silver("\\1"), out)
out <- gsub("([.]?0+)$", font_white("\\1"), out)
if (any(out %like% "[.]", na.rm = TRUE)) {
out <- gsub("([.]?0+)$", font_white("\\1"), out)
}
create_pillar_column(out, align = "right", width = max(nchar(pasted)))
}

2
R/rsi.R
View File

@ -67,7 +67,7 @@
#'
#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
#'
#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
#'
#' ## After Interpretation
#'