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(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

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dr. M.S. (Matthijs) Berends
2024-07-16 14:51:57 +02:00
parent 4f9db23684
commit 640888f408
191 changed files with 321091 additions and 89382 deletions
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39
R/antibiogram.R
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@ -6,9 +6,9 @@
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
@ -392,14 +392,17 @@ antibiogram <- function(x,
} else {
out$numerator <- out$S
}
if (any(out$total < minimum, na.rm = TRUE)) {
if (all(out$total < minimum, na.rm = TRUE)) {
warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")
return(as_original_data_class(data.frame(), class(out), extra_class = "antibiogram"))
} else if (any(out$total < minimum, na.rm = TRUE)) {
if (isTRUE(info)) {
message_("NOTE: ", sum(out$total < minimum, na.rm = TRUE), " combinations had less than `minimum = ", minimum, "` results and were ignored", add_fn = font_red)
}
out <- out %pm>%
subset(total >= minimum)
}
# regroup for summarising
if (isTRUE(has_syndromic_group)) {
colnames(out)[1] <- "syndromic_group"
@ -409,9 +412,10 @@ antibiogram <- function(x,
out <- out %pm>%
pm_group_by(mo, ab)
}
out <- out %pm>%
pm_summarise(SI = numerator / total)
# transform names of antibiotics
ab_naming_function <- function(x, t, l, s) {
x <- strsplit(x, s, fixed = TRUE)
@ -515,6 +519,29 @@ antibiogram <- function(x,
)
}
# will be exported in R/zzz.R
tbl_sum.antibiogram <- function(x, ...) {
if (isTRUE(base::l10n_info()$`UTF-8`)) {
cross <- "\u00d7"
} else {
cross <- "x"
}
dims <- paste(format(NROW(x), big.mark = ","), cross, format(NCOL(x), big.mark = ","))
names(dims) <- "An Antibiogram"
dims
}
# will be exported in R/zzz.R
tbl_format_footer.antibiogram <- function(x, ...) {
footer <- NextMethod()
if (NROW(x) == 0) {
return(footer)
}
c(footer, font_subtle(paste0("# Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,\n",
"# or use it directly in R Markdown or ",
font_url("https://quarto.org", "Quarto"), ", see ", word_wrap("?antibiogram"))))
}
#' @export
#' @rdname antibiogram
plot.antibiogram <- function(x, ...) {