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(v1.3.0.9016) mo_uncertainties() overhaul

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dr. M.S. (Matthijs) Berends 2020-09-12 08:49:01 +02:00
parent 68e9cb78e9
commit 3ff871afeb
71 changed files with 820 additions and 169 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.3.0.9015
Date: 2020-09-03
Version: 1.3.0.9016
Date: 2020-09-12
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

6
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.3.0.9015
## <small>Last updated: 3 September 2020</small>
# AMR 1.3.0.9016
## <small>Last updated: 12 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
@ -39,6 +39,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
#> [1] 24 24
```
* Improvements for `as.mo()`:
* Any user input value that could mean more than one taxonomic entry is now considered 'uncertain'. Instead of a warning, a message will be thrown and the accompanying `mo_uncertainties()` has been changed completely; it now prints all possible candidates with their score.
* Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using `mo_*` functions like `mo_name()` on microoganism IDs.
* Added parameter `ignore_pattern` to `as.mo()` which can also be given to `mo_*` functions like `mo_name()`, to exclude known non-relevant input from analysing. This can also be set with the option `AMR_ignore_pattern`.
* `get_locale()` now uses `Sys.getlocale()` instead of `Sys.getlocale("LC_COLLATE")`
@ -48,6 +49,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
* BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
* Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: `tibble` printing support for classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`. When using `tibble`s containing antimicrobial columns (class `<rsi>`), "S" will print in green, "I" will print in yellow and "R" will print in red. Microbial IDs (class `<mo>`) will emphasise on the genus and species, not on the kingdom.
* Names of antiviral agents in data set `antivirals` now have a starting capital letter, like it is the case in the `antibiotics` data set
* Updated the documentation of the `WHONET` data set to clarify that all patient names are fictitious
### Other
* Removed unnecessary references to the `base` package

3
R/aa_helper_functions.R
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@ -492,7 +492,8 @@ create_pillar_column <- function(x, ...) {
}
}
# copied from vctrs::s3_register by their permission
# copied from vctrs::s3_register by their permission:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register <- function(generic, class, method = NULL) {
stopifnot(is.character(generic), length(generic) == 1)
stopifnot(is.character(class), length(class) == 1)

13
R/amr.R
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@ -68,3 +68,16 @@
#' @name AMR
#' @rdname AMR
NULL
#' Plotting for classes `rsi` and `disk`
#'
#' Functions to print classes of the `AMR` package.
#' @inheritSection lifecycle Stable lifecycle
#' @inheritSection AMR Read more on our website!
#' @param ... Parameters passed on to functions
#' @inheritParams base::plot
#' @inheritParams graphics::barplot
#' @name plot
#' @rdname plot
#' @keywords internal
NULL

2
R/data.R
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@ -194,7 +194,7 @@ catalogue_of_life <- list(
#' Data set with `r format(nrow(WHONET), big.mark = ",")` isolates - WHONET example
#'
#' This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our [example_isolates] data set. All patient names are created using online surname generators and are only in place for practice purposes.
#' This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our [example_isolates] data set. All patient names are created using online surname generators and are only in place for practice purposes.
#' @format A [`data.frame`] with `r format(nrow(WHONET), big.mark = ",")` observations and `r ncol(WHONET)` variables:
#' - `Identification number`\cr ID of the sample
#' - `Specimen number`\cr ID of the specimen

4
R/mic.R
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@ -210,7 +210,7 @@ summary.mic <- function(object, ...) {
#' @method plot mic
#' @export
#' @importFrom graphics barplot axis par
#' @noRd
#' @rdname plot
plot.mic <- function(x,
main = paste("MIC values of", deparse(substitute(x))),
ylab = "Frequency",
@ -229,7 +229,7 @@ plot.mic <- function(x,
#' @method barplot mic
#' @export
#' @importFrom graphics barplot axis
#' @noRd
#' @rdname plot
barplot.mic <- function(height,
main = paste("MIC values of", deparse(substitute(height))),
ylab = "Frequency",

155
R/mo.R
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@ -86,7 +86,7 @@
#' - `"Fluoroquinolone-resistant Neisseria gonorrhoeae"`. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result *Neisseria gonorrhoeae* (``r as.mo("Neisseria gonorrhoeae")``) needs review.
#'
#' There are three helper functions that can be run after using the [as.mo()] function:
#' - Use [mo_uncertainties()] to get a [`data.frame`] with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where *n* is the number of characters of the full taxonomic name of the microorganism, and *L* is the [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) between that full name and the user input.
#' - Use [mo_uncertainties()] to get a [`data.frame`] that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) between the full taxonomic name and the user input.
#' - Use [mo_failures()] to get a [`character`] [`vector`] with all values that could not be coerced to a valid value.
#' - Use [mo_renamed()] to get a [`data.frame`] with all values that could be coerced based on old, previously accepted taxonomic names.
#'
@ -178,6 +178,14 @@ as.mo <- function(x,
...) {
check_dataset_integrity()
if (tryCatch(all(x %in% MO_lookup$mo, na.rm = TRUE)
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# don't look into valid MO codes, just return them
# is.mo() won't work - codes might change between package versions
return(to_class_mo(x))
}
if (tryCatch(all(tolower(x) %in% MO_lookup$fullname_lower, na.rm = TRUE)
& isFALSE(Becker)
@ -273,36 +281,7 @@ exec_as.mo <- function(x,
reference_data_to_use = MO_lookup) {
check_dataset_integrity()
lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug) {
# `column` can be NULL for all columns, or a selection
# returns a character (vector) - if `column` > length 1 then with columns as names
if (isTRUE(debug_mode)) {
cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
}
if (length(column) == 1) {
res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), column, drop = TRUE]
res <- as.character(res)
if (length(res) == 0) {
NA_character_
} else {
res[seq_len(min(n, length(res)))]
}
} else {
if (is.null(column)) {
column <- names(haystack)
}
res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
if (NROW(res) == 0) {
res <- rep(NA_character_, length(column))
}
res <- as.character(res)
names(res) <- column
res
}
}
# start off with replaced language-specific non-ASCII characters with ASCII characters
x <- parse_and_convert(x)
# replace mo codes used in older package versions
@ -323,14 +302,15 @@ exec_as.mo <- function(x,
}
options(mo_renamed_last_run = NULL)
failures <- character(0)
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
uncertainties <- data.frame(uncertainty = integer(0),
input = character(0),
fullname = character(0),
renamed_to = character(0),
mo = character(0),
mo = character(0),
candidates = character(0),
stringsAsFactors = FALSE)
failures <- character(0)
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
old_mo_warning <- FALSE
x_input <- x
@ -403,6 +383,43 @@ exec_as.mo <- function(x,
} else if (!all(x %in% microorganisms[, property])) {
lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
# `column` can be NULL for all columns, or a selection
# returns a character (vector) - if `column` > length 1 then with columns as names
if (isTRUE(debug_mode)) {
cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
}
if (length(column) == 1) {
res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
res <- as.character(res_df[, column, drop = TRUE])
if (length(res) == 0) {
NA_character_
} else {
if (length(res) > n) {
# save the other possible results as well
uncertainties <<- rbind(uncertainties,
format_uncertainty_as_df(uncertainty_level = 1,
input = x_backup[i],
result_mo = res_df[1, "mo", drop = TRUE],
candidates = as.character(res_df[, "fullname", drop = TRUE])))
}
res[seq_len(min(n, length(res)))]
}
} else {
if (is.null(column)) {
column <- names(haystack)
}
res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
if (NROW(res) == 0) {
res <- rep(NA_character_, length(column))
}
res <- as.character(res)
names(res) <- column
res
}
}
strip_whitespace <- function(x, dyslexia_mode) {
# all whitespaces (tab, new lines, etc.) should be one space
# and spaces before and after should be omitted
@ -1387,9 +1404,7 @@ exec_as.mo <- function(x,
}
msg <- paste0("Result", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1],
" ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
warning(font_red(paste0("\n", msg)),
call. = FALSE,
immediate. = TRUE) # thus will always be shown, even if >= warnings
message(font_blue(msg))
}
# Becker ----
@ -1514,25 +1529,25 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
format_uncertainty_as_df <- function(uncertainty_level,
input,
result_mo) {
result_mo,
candidates = NULL) {
if (!is.null(getOption("mo_renamed_last_run", default = NULL))) {
# was found as a renamed mo
df <- data.frame(uncertainty = uncertainty_level,
input = input,
fullname = getOption("mo_renamed_last_run"),
renamed_to = MO_lookup[which(MO_lookup$mo == result_mo), "fullname"][1],
mo = result_mo,
stringsAsFactors = FALSE)
fullname <- getOption("mo_renamed_last_run")
options(mo_renamed_last_run = NULL)
renamed_to <- MO_lookup[match(result_mo, MO_lookup$mo), "fullname", drop = TRUE][1]
} else {
df <- data.frame(uncertainty = uncertainty_level,
input = input,
fullname = MO_lookup[which(MO_lookup$mo == result_mo), "fullname"][1],
renamed_to = NA_character_,
mo = result_mo,
stringsAsFactors = FALSE)
fullname <- MO_lookup[match(result_mo, MO_lookup$mo), "fullname", drop = TRUE][1]
renamed_to <- NA_character_
}
df
data.frame(uncertainty = uncertainty_level,
input = input,
fullname = fullname,
renamed_to = renamed_to,
mo = result_mo,
# save max 25 entries
candidates = if (length(candidates) > 1) paste(candidates[c(2:min(25, length(candidates)))], collapse = ", ") else "",
stringsAsFactors = FALSE)
}
# will be exported using s3_register() in R/zzz.R
@ -1714,13 +1729,27 @@ print.mo_uncertainties <- function(x, ...) {
colour1 <- font_red
colour2 <- function(...) font_red_bg(font_white(...))
}
if (x[i, "candidates"] != "") {
candidates <- unlist(strsplit(x[i, "candidates"], ", ", fixed = TRUE))
scores <- finding_score(x[i, "input"], candidates)
# sort on descending scores
candidates <- candidates[order(1 - scores)]
candidates <- paste0(font_italic(candidates, collapse = NULL),
" (", trimws(percentage(scores[order(1 - scores)], digits = 1)), ")")
candidates <- paste(candidates, collapse = ", ")
# align with input after arrow
candidates <- paste0("\n", strrep(" ", nchar(x[i, "input"]) + 12), "Other: ", candidates)
} else {
candidates <- ""
}
msg <- paste(msg,
paste0(colour2(paste0(" [", x[i, "uncertainty"], "] ")), ' "', x[i, "input"], '" -> ',
colour1(paste0(font_italic(x[i, "fullname"]),
ifelse(!is.na(x[i, "renamed_to"]), paste(", renamed to", font_italic(x[i, "renamed_to"])), ""),
" (", x[i, "mo"],
", score: ", percentage(levenshtein_fraction(x[i, "input"], x[i, "fullname"]), digits = 1),
")"))),
", score: ", trimws(percentage(finding_score(x[i, "input"], x[i, "fullname"]), digits = 1)),
")")),
candidates),
sep = "\n")
}
cat(msg)
@ -1729,7 +1758,7 @@ print.mo_uncertainties <- function(x, ...) {
#' @rdname as.mo
#' @export
mo_renamed <- function() {
items <- getOption("mo_renamed")
items <- getOption("mo_renamed", default = NULL)
if (is.null(items)) {
items <- data.frame()
} else {
@ -1805,15 +1834,25 @@ load_mo_failures_uncertainties_renamed <- function(metadata) {
options("mo_renamed" = metadata$renamed)
}
levenshtein_fraction <- function(input, output) {
finding_score <- function(input, output) {
# output is always a valid fullname
levenshtein <- double(length = length(input))
if (length(output) == 1) {
output <- rep(output, length(input))
}
if (length(input) == 1) {
input <- rep(input, length(output))
}
for (i in seq_len(length(input))) {
# determine Levenshtein distance, but maximise to nchar of output
levenshtein[i] <- min(as.double(utils::adist(input[i], output[i], ignore.case = TRUE)),
nchar(output[i]))
nchar(output[i]))
}
# self-made score between 0 and 1 (for % certainty, so 0 means huge distance, 1 means no distance)
(nchar(output) - 0.5 * levenshtein) / nchar(output)
dist <- (nchar(output) - 0.5 * levenshtein) / nchar(output)
index_in_MO_lookup <- tryCatch((nrow(MO_lookup) - match(output, MO_lookup$fullname)) / nrow(MO_lookup),
error = function(e) rep(1, length(output)))
dist * index_in_MO_lookup
}
trimws2 <- function(x) {

4
R/rsi.R
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@ -755,7 +755,7 @@ summary.rsi <- function(object, ...) {
#' @method plot rsi
#' @export
#' @importFrom graphics text axis
#' @noRd
#' @rdname plot
plot.rsi <- function(x,
lwd = 2,
ylim = NULL,
@ -812,7 +812,7 @@ plot.rsi <- function(x,
#' @method barplot rsi
#' @export
#' @importFrom graphics barplot axis par
#' @noRd
#' @rdname plot
barplot.rsi <- function(height,
col = c("chartreuse4", "chartreuse3", "brown3"),
xlab = ifelse(beside, "Antimicrobial Interpretation", ""),

15
R/translate.R
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@ -63,13 +63,18 @@
#' mo_name("CoNS", language = "pt")
#' #> "Staphylococcus coagulase negativo (CoNS)"
get_locale <- function() {
# AMR versions prior to 1.3.0 used the environmental variable:
if (!identical("", Sys.getenv("AMR_locale"))) {
options(AMR_locale = Sys.getenv("AMR_locale"))
}
if (!is.null(getOption("AMR_locale", default = NULL))) {
if (!language %in% LANGUAGES_SUPPORTED) {
stop_("unsupported language: '", language, "' - use one of: ",
paste0("'", LANGUAGES_SUPPORTED, "'", collapse = ", "),
call = FALSE)
lang <- getOption("AMR_locale")
if (lang %in% LANGUAGES_SUPPORTED) {
return(lang)
} else {
return(getOption("AMR_locale"))
stop_("unsupported language: '", lang, "' - use one of: ",
paste0("'", LANGUAGES_SUPPORTED, "'", collapse = ", "))
}
}

5
R/zzz.R
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@ -32,8 +32,9 @@
value = sort(c("en", unique(translations_file$lang))),
envir = asNamespace("AMR"))
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft) without the need to depend on other packages
# this was suggested by the developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("tibble::type_sum", "ab")
s3_register("pillar::pillar_shaft", "mo")

1
_pkgdown.yml
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@ -138,6 +138,7 @@ reference:
- "`as.mic`"
- "`as.disk`"
- "`eucast_rules`"
- "`plot`"
- title: "Analysing data: antimicrobial resistance"
desc: >

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data-raw/country_analysis.R
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@ -168,7 +168,8 @@ data %>%
left_join(ip_tbl, by = c("ipaddress" = "ip")) %>%
group_by(country = countrycode::countrycode(country,
origin = 'iso2c',
destination = 'country.name')) %>%
destination = 'country.name',
custom_match = c(XK = "Kosovo"))) %>%
summarise(first = min(timestamp_server)) %>%
arrange(desc(first)) %>%
mutate(frame = case_when(first <= as.POSIXct("2019-06-30") ~ "Q1-Q2 2019",

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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>

142
docs/articles/benchmarks.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -226,22 +226,82 @@
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
times = <span class="fl">10</span>)
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Results of three values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 12.0 12.0 24.0 15.0 40.0 43.0</span>
<span class="co"># as.mo("stau") 170.0 170.0 190.0 180.0 210.0 250.0</span>
<span class="co"># as.mo("STAU") 160.0 180.0 200.0 190.0 220.0 230.0</span>
<span class="co"># as.mo("staaur") 9.4 11.0 21.0 13.0 40.0 48.0</span>
<span class="co"># as.mo("STAAUR") 9.0 13.0 34.0 14.0 43.0 140.0</span>
<span class="co"># as.mo("S. aureus") 16.0 18.0 20.0 19.0 21.0 25.0</span>
<span class="co"># as.mo("S aureus") 15.0 16.0 20.0 18.0 21.0 39.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.1 1.1 1.4 1.6 1.6 1.7</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 920.0 950.0 940.0 980.0 1000.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 390.0 410.0 440.0 440.0 460.0 490.0</span>
<span class="co"># as.mo("MRSA") 11.0 12.0 30.0 13.0 40.0 130.0</span>
<span class="co"># as.mo("VISA") 16.0 18.0 30.0 20.0 46.0 69.0</span>
<span class="co"># as.mo("VRSA") 14.0 19.0 33.0 33.0 47.0 51.0</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 9.9 13.0 24.0 17.0 39.0 45</span>
<span class="co"># as.mo("stau") 200.0 210.0 240.0 240.0 260.0 290</span>
<span class="co"># as.mo("STAU") 190.0 220.0 230.0 220.0 260.0 270</span>
<span class="co"># as.mo("staaur") 9.4 13.0 26.0 15.0 44.0 47</span>
<span class="co"># as.mo("STAAUR") 9.3 11.0 18.0 14.0 15.0 45</span>
<span class="co"># as.mo("S. aureus") 21.0 25.0 30.0 26.0 26.0 50</span>
<span class="co"># as.mo("S aureus") 25.0 47.0 48.0 51.0 56.0 64</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.5 1.9 2.3 2.4 2.5 3</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 860.0 900.0 930.0 920.0 950.0 1100</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 410.0 420.0 430.0 430.0 450.0 460</span>
<span class="co"># as.mo("MRSA") 12.0 13.0 16.0 14.0 15.0 41</span>
<span class="co"># as.mo("VISA") 15.0 21.0 38.0 22.0 47.0 130</span>
<span class="co"># as.mo("VRSA") 18.0 20.0 25.0 22.0 22.0 47</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -286,9 +346,9 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 90.3 101 120 102 141 202 10</span>
<span class="co"># mo_name(x) 96.1 123 140 133 144 251 10</span>
</pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.102 seconds. You only lose time on your unique input values.</p>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.133 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -299,14 +359,24 @@
B = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
C = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
times = <span class="fl">10</span>)
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.08 7.29 8.00 8.25 8.49 9.22 10</span>
<span class="co"># B 12.30 13.50 14.20 14.50 14.70 14.80 10</span>
<span class="co"># C 2.14 2.26 7.35 2.38 2.51 52.30 10</span>
<span class="co"># A 7.83 7.96 8.19 8.22 8.33 8.84 10</span>
<span class="co"># B 18.10 19.50 27.80 20.20 20.70 65.90 10</span>
<span class="co"># C 1.77 2.11 2.34 2.27 2.33 3.22 10</span>
</pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0024 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0023 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -320,14 +390,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.29 1.38 1.64 1.47 1.84 2.28 10</span>
<span class="co"># B 1.27 1.62 1.76 1.69 1.82 2.71 10</span>
<span class="co"># C 1.28 1.32 1.56 1.48 1.77 2.09 10</span>
<span class="co"># D 1.29 1.46 1.68 1.66 1.77 2.24 10</span>
<span class="co"># E 1.26 1.39 5.34 1.64 1.77 39.00 10</span>
<span class="co"># F 1.26 1.33 1.58 1.44 1.80 2.14 10</span>
<span class="co"># G 1.32 1.51 1.65 1.68 1.75 2.05 10</span>
<span class="co"># H 1.31 1.43 1.71 1.68 1.86 2.49 10</span>
<span class="co"># A 1.56 1.62 5.61 1.93 2.26 38.90 10</span>
<span class="co"># B 1.50 1.72 1.88 1.90 2.01 2.34 10</span>
<span class="co"># C 1.52 1.76 1.88 1.89 1.96 2.27 10</span>
<span class="co"># D 1.47 1.62 1.85 1.86 1.89 2.80 10</span>
<span class="co"># E 1.51 1.84 1.98 1.88 2.07 2.56 10</span>
<span class="co"># F 1.44 1.50 1.68 1.57 1.89 2.19 10</span>
<span class="co"># G 1.47 1.48 1.65 1.59 1.84 2.00 10</span>
<span class="co"># H 1.55 1.60 1.75 1.69 1.81 2.34 10</span>
</pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
@ -356,13 +426,13 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 13.29 13.54 17.53 13.70 14.93 58.25 100</span>
<span class="co"># de 14.25 14.46 19.09 14.69 16.23 58.96 100</span>
<span class="co"># nl 17.89 18.46 24.37 19.05 21.14 70.25 100</span>
<span class="co"># es 14.05 14.41 18.08 14.72 16.11 57.07 100</span>
<span class="co"># it 14.07 14.38 19.18 14.63 16.40 58.14 100</span>
<span class="co"># fr 13.98 14.42 17.30 14.57 15.31 56.81 100</span>
<span class="co"># pt 13.95 14.38 17.78 14.60 16.32 57.53 100</span>
<span class="co"># en 13.84 14.04 20.10 14.54 16.47 59.20 100</span>
<span class="co"># de 14.79 15.10 20.00 15.76 17.64 63.37 100</span>
<span class="co"># nl 18.52 19.35 24.11 21.44 22.93 62.12 100</span>
<span class="co"># es 14.72 15.02 20.10 16.06 17.90 60.60 100</span>
<span class="co"># it 14.61 14.93 18.06 15.45 17.33 52.47 100</span>
<span class="co"># fr 14.73 15.02 21.06 15.62 18.09 69.54 100</span>
<span class="co"># pt 14.74 14.99 21.19 16.17 17.88 64.71 100</span>
</pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -210,7 +210,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘snomed’</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2020 11:07:11 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 3 September 2020 20:59:45 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds" target="_blank"><img src="download_rds.png" width="50px" title="2.7 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="6.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt" target="_blank"><img src="download_txt.png" width="50px" title="13.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas" target="_blank"><img src="download_sas.png" width="50px" title="26.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav" target="_blank"><img src="download_sav.png" width="50px" title="28.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta" target="_blank"><img src="download_dta.png" width="50px" title="25.2 MB"></a></p>
<div id="source" class="section level3">
<h3 class="hasAnchor">

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>

2
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>

20
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309015" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9015">
<a href="#amr-1309015" class="anchor"></a>AMR 1.3.0.9015<small> Unreleased </small>
<div id="amr-1309016" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9016">
<a href="#amr-1309016" class="anchor"></a>AMR 1.3.0.9016<small> Unreleased </small>
</h1>
<div id="last-updated-3-september-2020" class="section level2">
<div id="last-updated-12-september-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-3-september-2020" class="anchor"></a><small>Last updated: 3 September 2020</small>
<a href="#last-updated-12-september-2020" class="anchor"></a><small>Last updated: 12 September 2020</small>
</h2>
<p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
<div id="new" class="section level3">
@ -299,6 +299,7 @@
<li>
<p>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</p>
<ul>
<li>Any user input value that could mean more than one taxonomic entry is now considered ‘uncertain’. Instead of a warning, a message will be thrown and the accompanying <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> has been changed completely; it now prints all possible candidates with their score.</li>
<li>Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using <code>mo_*</code> functions like <code><a href="../reference/mo_property.html">mo_name()</a></code> on microoganism IDs.</li>
<li>Added parameter <code>ignore_pattern</code> to <code><a href="../reference/as.mo.html">as.mo()</a></code> which can also be given to <code>mo_*</code> functions like <code><a href="../reference/mo_property.html">mo_name()</a></code>, to exclude known non-relevant input from analysing. This can also be set with the option <code>AMR_ignore_pattern</code>.</li>
</ul>
@ -310,6 +311,7 @@
<li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
<li><p>Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: <code>tibble</code> printing support for classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and <code>&lt;mo&gt;</code>. When using <code>tibble</code>s containing antimicrobial columns (class <code>&lt;rsi&gt;</code>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class <code>&lt;mo&gt;</code>) will emphasise on the genus and species, not on the kingdom.</p></li>
<li><p>Names of antiviral agents in data set <code>antivirals</code> now have a starting capital letter, like it is the case in the <code>antibiotics</code> data set</p></li>
<li><p>Updated the documentation of the <code>WHONET</code> data set to clarify that all patient names are fictitious</p></li>
</ul>
</div>
<div id="other" class="section level3">
@ -961,7 +963,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><a href="https://rdrr.io/r/graphics/plot.default.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> for MIC and RSI classes</li>
<li>Small improvements to <code><a href="../reference/plot.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> for MIC and RSI classes</li>
<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
</ul>
@ -1169,10 +1171,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</p></li>
<li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</p></li>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/graphics/plot.default.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="../reference/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb24"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">septic_patients</span>, col_ab = <span class="st">"amox"</span>)
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span>(<span class="kw">x</span>)
<span class="fu"><a href="../reference/plot.html">plot</a></span>(<span class="kw">x</span>)
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">x</span>)
</pre></div>
</li>

2
docs/pkgdown.yml
View File

@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-09-03T18:57Z
last_built: 2020-09-12T06:48Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

6
docs/reference/WHONET.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes." />
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
</div>
<pre class="usage"><span class='kw'>WHONET</span></pre>

5
docs/reference/ab_property.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -384,7 +384,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

5
docs/reference/as.ab.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -344,7 +344,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
<span class='co'># they use as.ab() internally:</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

5
docs/reference/as.disk.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -300,7 +300,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>df</span>)
}</pre>
}
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

7
docs/reference/as.mic.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -298,8 +298,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
ab = <span class='st'>"AMX"</span>,
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>mic_data</span>)</pre>
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>mic_data</span>)
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

7
docs/reference/as.mo.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -347,7 +347,7 @@
</ul>
<p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul>
<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \((n - 0.5 * L) / n\), where <em>n</em> is the number of characters of the full taxonomic name of the microorganism, and <em>L</em> is the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between that full name and the user input.</p></li>
<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between the full taxonomic name and the user input.</p></li>
<li><p>Use <code>mo_failures()</code> to get a <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with all values that could not be coerced to a valid value.</p></li>
<li><p>Use <code>mo_renamed()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that could be coerced based on old, previously accepted taxonomic names.</p></li>
</ul>
@ -456,7 +456,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='co'># although this works easier and does the same:</span>
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(mo = <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>)))
}</pre>
}
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

13
docs/reference/as.rsi.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -340,12 +340,14 @@
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
</pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.disk</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
</pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
@ -468,7 +470,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>rsi_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='fu'>is.rsi</span>(<span class='kw'>rsi_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
@ -487,7 +489,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>, threshold = <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
}</pre>
}
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

5
docs/reference/atc_online.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -333,7 +333,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># [2] "ANTIBACTERIALS FOR SYSTEMIC USE"</span>
<span class='co'># [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
<span class='co'># [4] "Penicillins with extended spectrum"</span>
}</pre>
}
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

5
docs/reference/bug_drug_combinations.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -355,7 +355,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>),
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span>))
<span class='co'># }</span></pre>
<span class='co'># }</span>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

8
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -444,6 +444,12 @@
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
</td>
<td><p>Apply EUCAST rules</p></td>
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for classes <code>rsi</code> and <code>disk</code></p></td>
</tr>
</tbody><tbody>
<tr>

5
docs/reference/like.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -317,7 +317,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"^ent"</span>)
}</pre>
}
</pre>
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2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -461,7 +461,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
<span class='co'># get a list with the taxonomy, the authors, Gram-stain and URL to the online database</span>
<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
<span class='co'># }</span></pre>
<span class='co'># }</span>
</pre>
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<h1>Plotting for classes <code>rsi</code> and <code>disk</code></h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<div class="hidden name"><code>plot.Rd</code></div>
</div>
<div class="ref-description">
<p>Functions to print classes of the <code>AMR</code> package.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mic</span>
<span class='fu'>plot</span>(
<span class='kw'>x</span>,
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>))),
ylab = <span class='st'>"Frequency"</span>,
xlab = <span class='st'>"MIC value"</span>,
axes = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='co'># S3 method for mic</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(
<span class='kw'>height</span>,
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>height</span>))),
ylab = <span class='st'>"Frequency"</span>,
xlab = <span class='st'>"MIC value"</span>,
axes = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='co'># S3 method for rsi</span>
<span class='fu'>plot</span>(
<span class='kw'>x</span>,
lwd = <span class='fl'>2</span>,
ylim = <span class='kw'>NULL</span>,
ylab = <span class='st'>"Percentage"</span>,
xlab = <span class='st'>"Antimicrobial Interpretation"</span>,
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>))),
axes = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='co'># S3 method for rsi</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(
<span class='kw'>height</span>,
col = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"chartreuse4"</span>, <span class='st'>"chartreuse3"</span>, <span class='st'>"brown3"</span>),
xlab = <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>beside</span>, <span class='st'>"Antimicrobial Interpretation"</span>, <span class='st'>""</span>),
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>height</span>))),
ylab = <span class='st'>"Frequency"</span>,
beside = <span class='fl'>TRUE</span>,
axes = <span class='kw'>beside</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>the coordinates of points in the plot. Alternatively, a
single plotting structure, function or <em>any <span style="R">R</span> object with a
<code>plot</code> method</em> can be provided.</p></td>
</tr>
<tr>
<th>main</th>
<td><p>overall and sub title for the plot.</p></td>
</tr>
<tr>
<th>ylab</th>
<td><p>a label for the y axis.</p></td>
</tr>
<tr>
<th>xlab</th>
<td><p>a label for the x axis.</p></td>
</tr>
<tr>
<th>axes</th>
<td><p>logical. If <code>TRUE</code>, a vertical (or horizontal, if
<code>horiz</code> is true) axis is drawn.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Parameters passed on to functions</p></td>
</tr>
<tr>
<th>height</th>
<td><p>either a vector or matrix of values describing the
bars which make up the plot. If <code>height</code> is a vector, the
plot consists of a sequence of rectangular bars with heights
given by the values in the vector. If <code>height</code> is a matrix
and <code>beside</code> is <code>FALSE</code> then each bar of the plot
corresponds to a column of <code>height</code>, with the values in the
column giving the heights of stacked sub-bars making up the
bar. If <code>height</code> is a matrix and <code>beside</code> is
<code>TRUE</code>, then the values in each column are juxtaposed
rather than stacked.</p></td>
</tr>
<tr>
<th>ylim</th>
<td><p>limits for the y axis.</p></td>
</tr>
<tr>
<th>col</th>
<td><p>a vector of colors for the bars or bar components.
By default, grey is used if <code>height</code> is a vector, and a
gamma-corrected grey palette if <code>height</code> is a matrix.</p></td>
</tr>
<tr>
<th>beside</th>
<td><p>a logical value. If <code>FALSE</code>, the columns of
<code>height</code> are portrayed as stacked bars, and if <code>TRUE</code>
the columns are portrayed as juxtaposed bars.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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5
docs/reference/translate.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
</span>
</div>
@ -291,7 +291,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># Portuguese</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"pt"</span>)
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span></pre>
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span>
</pre>
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@ -135,6 +135,9 @@
<url>
<loc>https://msberends.github.io/AMR/reference/pca.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR/reference/plot.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR/reference/proportion.html</loc>
</url>

2
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
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</span>
</div>

2
man/WHONET.Rd
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@ -39,7 +39,7 @@ A \code{\link{data.frame}} with 500 observations and 53 variables:
WHONET
}
\description{
This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our \link{example_isolates} data set. All patient names are created using online surname generators and are only in place for practice purposes.
This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our \link{example_isolates} data set. All patient names are created using online surname generators and are only in place for practice purposes.
}
\section{Reference data publicly available}{

2
man/as.mo.Rd
View File

@ -106,7 +106,7 @@ With the default setting (\code{allow_uncertain = TRUE}, level 2), below example
There are three helper functions that can be run after using the \code{\link[=as.mo]{as.mo()}} function:
\itemize{
\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \code{\link{data.frame}} with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where \emph{n} is the number of characters of the full taxonomic name of the microorganism, and \emph{L} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} between that full name and the user input.
\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \code{\link{data.frame}} that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} between the full taxonomic name and the user input.
\item Use \code{\link[=mo_failures]{mo_failures()}} to get a \code{\link{character}} \code{\link{vector}} with all values that could not be coerced to a valid value.
\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \code{\link{data.frame}} with all values that could be coerced based on old, previously accepted taxonomic names.
}

104
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@ -0,0 +1,104 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/amr.R, R/mic.R, R/rsi.R
\name{plot}
\alias{plot}
\alias{plot.mic}
\alias{barplot.mic}
\alias{plot.rsi}
\alias{barplot.rsi}
\title{Plotting for classes \code{rsi} and \code{disk}}
\usage{
\method{plot}{mic}(
x,
main = paste("MIC values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "MIC value",
axes = FALSE,
...
)
\method{barplot}{mic}(
height,
main = paste("MIC values of", deparse(substitute(height))),
ylab = "Frequency",
xlab = "MIC value",
axes = FALSE,
...
)
\method{plot}{rsi}(
x,
lwd = 2,
ylim = NULL,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = paste("Resistance Overview of", deparse(substitute(x))),
axes = FALSE,
...
)
\method{barplot}{rsi}(
height,
col = c("chartreuse4", "chartreuse3", "brown3"),
xlab = ifelse(beside, "Antimicrobial Interpretation", ""),
main = paste("Resistance Overview of", deparse(substitute(height))),
ylab = "Frequency",
beside = TRUE,
axes = beside,
...
)
}
\arguments{
\item{x}{the coordinates of points in the plot. Alternatively, a
single plotting structure, function or \emph{any \R object with a
\code{plot} method} can be provided.}
\item{main}{overall and sub title for the plot.}
\item{ylab}{a label for the y axis.}
\item{xlab}{a label for the x axis.}
\item{axes}{logical. If \code{TRUE}, a vertical (or horizontal, if
\code{horiz} is true) axis is drawn.}
\item{...}{Parameters passed on to functions}
\item{height}{either a vector or matrix of values describing the
bars which make up the plot. If \code{height} is a vector, the
plot consists of a sequence of rectangular bars with heights
given by the values in the vector. If \code{height} is a matrix
and \code{beside} is \code{FALSE} then each bar of the plot
corresponds to a column of \code{height}, with the values in the
column giving the heights of stacked sub-bars making up the
bar. If \code{height} is a matrix and \code{beside} is
\code{TRUE}, then the values in each column are juxtaposed
rather than stacked.}
\item{ylim}{limits for the y axis.}
\item{col}{a vector of colors for the bars or bar components.
By default, grey is used if \code{height} is a vector, and a
gamma-corrected grey palette if \code{height} is a matrix.}
\item{beside}{a logical value. If \code{FALSE}, the columns of
\code{height} are portrayed as stacked bars, and if \code{TRUE}
the columns are portrayed as juxtaposed bars.}
}
\description{
Functions to print classes of the \code{AMR} package.
}
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\keyword{internal}

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10
tests/testthat/test-mo.R
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@ -201,12 +201,12 @@ test_that("as.mo works", {
print(mo_renamed())
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS")
expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS")
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",