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(v1.5.0.9026) vignette update, support for GISA

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dr. M.S. (Matthijs) Berends 2021-02-25 12:31:12 +01:00
parent a673407904
commit 1737d56ae4
36 changed files with 604 additions and 480 deletions
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1
.Rbuildignore
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@ -22,7 +22,6 @@
^data-raw$ ^data-raw$
^\.lintr$ ^\.lintr$
^tests/testthat/_snaps$ ^tests/testthat/_snaps$
^vignettes/AMR.Rmd$
^vignettes/benchmarks.Rmd$ ^vignettes/benchmarks.Rmd$
^vignettes/EUCAST.Rmd$ ^vignettes/EUCAST.Rmd$
^vignettes/PCA.Rmd$ ^vignettes/PCA.Rmd$

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.5.0.9025 Version: 1.5.0.9026
Date: 2021-02-25 Date: 2021-02-25
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

1
NAMESPACE
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@ -243,6 +243,7 @@ export(theme_rsi)
importFrom(graphics,arrows) importFrom(graphics,arrows)
importFrom(graphics,axis) importFrom(graphics,axis)
importFrom(graphics,barplot) importFrom(graphics,barplot)
importFrom(graphics,legend)
importFrom(graphics,mtext) importFrom(graphics,mtext)
importFrom(graphics,plot) importFrom(graphics,plot)
importFrom(graphics,points) importFrom(graphics,points)

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.5.0.9025 # AMR 1.5.0.9026
## <small>Last updated: 25 February 2021</small> ## <small>Last updated: 25 February 2021</small>
### New ### New
@ -63,6 +63,7 @@
* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package (e.g., `as.mo()` is now up to 4 times faster) * The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package (e.g., `as.mo()` is now up to 4 times faster)
* *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive * *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive
* `random_disk()` and `random_mic()` now have an expanded range in their randomisation * `random_disk()` and `random_mic()` now have an expanded range in their randomisation
* Support for GISA (glycopeptide-intermediate *S. aureus*), so e.g. `mo_genus("GISA")` will return `"Staphylococcus"`
### Other ### Other
* Big documentation updates * Big documentation updates

41
R/ggplot_rsi.R
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@ -36,7 +36,7 @@
#' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable #' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
#' @inheritParams proportion #' @inheritParams proportion
#' @param nrow (when using `facet`) number of rows #' @param nrow (when using `facet`) number of rows
#' @param colours a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be `FALSE` for standard [ggplot2][ggplot2::ggplot()] colours. The default colours are colour-blind friendly. #' @param colours a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be `FALSE` for standard [ggplot2][ggplot2::ggplot()] colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.
#' @param aesthetics aesthetics to apply the colours to, defaults to "fill" but can also be "colour" or "both" #' @param aesthetics aesthetics to apply the colours to, defaults to "fill" but can also be "colour" or "both"
#' @param datalabels show datalabels using [labels_rsi_count()] #' @param datalabels show datalabels using [labels_rsi_count()]
#' @param datalabels.size size of the datalabels #' @param datalabels.size size of the datalabels
@ -119,11 +119,6 @@
#' CIP) %>% #' CIP) %>%
#' ggplot_rsi(x = "age_group") #' ggplot_rsi(x = "age_group")
#' #'
#' # for colourblind mode, use divergent colours from the viridis package:
#' example_isolates %>%
#' select(AMX, NIT, FOS, TMP, CIP) %>%
#' ggplot_rsi() +
#' scale_fill_viridis_d()
#' # a shorter version which also adjusts data label colours: #' # a shorter version which also adjusts data label colours:
#' example_isolates %>% #' example_isolates %>%
#' select(AMX, NIT, FOS, TMP, CIP) %>% #' select(AMX, NIT, FOS, TMP, CIP) %>%
@ -155,11 +150,11 @@ ggplot_rsi <- function(data,
minimum = 30, minimum = 30,
language = get_locale(), language = get_locale(),
nrow = NULL, nrow = NULL,
colours = c(S = "#61a8ff", colours = c(S = "#3CAEA3",
SI = "#61a8ff", SI = "#3CAEA3",
I = "#61f7ff", I = "#F6D55C",
IR = "#ff6961", IR = "#ED553B",
R = "#ff6961"), R = "#ED553B"),
datalabels = TRUE, datalabels = TRUE,
datalabels.size = 2.5, datalabels.size = 2.5,
datalabels.colour = "grey15", datalabels.colour = "grey15",
@ -309,17 +304,19 @@ geom_rsi <- function(position = NULL,
x <- "interpretation" x <- "interpretation"
} }
ggplot2::layer(geom = "bar", stat = "identity", position = position, ggplot2::geom_col(
mapping = ggplot2::aes_string(x = x, y = y, fill = fill), data = function(x) {
params = list(...), data = function(x) { rsi_df(data = x,
rsi_df(data = x, translate_ab = translate_ab,
translate_ab = translate_ab, language = language,
language = language, minimum = minimum,
minimum = minimum, combine_SI = combine_SI,
combine_SI = combine_SI, combine_IR = combine_IR)
combine_IR = combine_IR) },
}) mapping = ggplot2::aes_string(x = x, y = y, fill = fill),
position = position,
...
)
} }
#' @rdname ggplot_rsi #' @rdname ggplot_rsi

6
R/globals.R
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@ -33,7 +33,10 @@ globalVariables(c(".rowid",
"atc_group1", "atc_group1",
"atc_group2", "atc_group2",
"code", "code",
"cols",
"count",
"data", "data",
"disk",
"dosage", "dosage",
"dose", "dose",
"dose_times", "dose_times",
@ -52,6 +55,7 @@ globalVariables(c(".rowid",
"language", "language",
"lookup", "lookup",
"method", "method",
"mic ",
"microorganism", "microorganism",
"microorganisms", "microorganisms",
"microorganisms.codes", "microorganisms.codes",
@ -67,8 +71,8 @@ globalVariables(c(".rowid",
"reference.rule", "reference.rule",
"reference.rule_group", "reference.rule_group",
"reference.version", "reference.version",
"rsi_translation",
"rowid", "rowid",
"rsi_translation",
"rule_group", "rule_group",
"rule_name", "rule_name",
"se_max", "se_max",

4
R/mo.R
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@ -711,8 +711,8 @@ exec_as.mo <- function(x,
} }
# translate known trivial abbreviations to genus + species ---- # translate known trivial abbreviations to genus + species ----
if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA") if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA", "GISA")
| x_backup_without_spp[i] %like_case% "(^| )(mrsa|mssa|visa|vrsa|borsa|la-?mrsa|ca-?mrsa)( |$)") { | x_backup_without_spp[i] %like_case% "(^| )(mrsa|mssa|visa|vrsa|borsa|gisa|la-?mrsa|ca-?mrsa)( |$)") {
x[i] <- lookup(fullname == "Staphylococcus aureus", uncertainty = -1) x[i] <- lookup(fullname == "Staphylococcus aureus", uncertainty = -1)
next next
} }

115
R/plot.R
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@ -28,7 +28,7 @@
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base R and `ggplot2`. #' Functions to plot classes `rsi`, `mic` and `disk`, with support for base R and `ggplot2`.
#' @inheritSection lifecycle Stable Lifecycle #' @inheritSection lifecycle Stable Lifecycle
#' @inheritSection AMR Read more on Our Website! #' @inheritSection AMR Read more on Our Website!
#' @param x MIC values created with [as.mic()] or disk diffusion values created with [as.disk()] #' @param x,data MIC values created with [as.mic()] or disk diffusion values created with [as.disk()]
#' @param mapping aesthetic mappings to use for [`ggplot()`][ggplot2::ggplot()] #' @param mapping aesthetic mappings to use for [`ggplot()`][ggplot2::ggplot()]
#' @param main,title title of the plot #' @param main,title title of the plot
#' @param xlab,ylab axis title #' @param xlab,ylab axis title
@ -37,7 +37,10 @@
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details* #' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
#' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly. #' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
#' @param expand logical to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled. #' @param expand logical to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
#' @details For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`. #' @details
#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
#'
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`.
#' #'
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. #' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
#' @name plot #' @name plot
@ -62,7 +65,7 @@
NULL NULL
#' @method plot mic #' @method plot mic
#' @importFrom graphics barplot axis mtext #' @importFrom graphics barplot axis mtext legend
#' @export #' @export
#' @rdname plot #' @rdname plot
plot.mic <- function(x, plot.mic <- function(x,
@ -89,13 +92,13 @@ plot.mic <- function(x,
x <- plot_prepare_table(x, expand = expand) x <- plot_prepare_table(x, expand = expand)
cols_sub <- plot_colours_and_sub(x = x, cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo, mo = mo,
ab = ab, ab = ab,
guideline = guideline, guideline = guideline,
colours_RSI = colours_RSI, colours_RSI = colours_RSI,
fn = as.mic, fn = as.mic,
...) ...)
barplot(x, barplot(x,
col = cols_sub$cols, col = cols_sub$cols,
@ -117,7 +120,7 @@ plot.mic <- function(x,
legend_col <- colours_RSI[2] legend_col <- colours_RSI[2]
} }
if (colours_RSI[3] %in% cols_sub$cols) { if (colours_RSI[3] %in% cols_sub$cols) {
legend_txt <- c(legend_txt, "Incr. exposure") legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3]) legend_col <- c(legend_col, colours_RSI[3])
} }
if (colours_RSI[1] %in% cols_sub$cols) { if (colours_RSI[1] %in% cols_sub$cols) {
@ -194,21 +197,21 @@ ggplot.mic <- function(data,
title <- gsub(" +", " ", paste0(title, collapse = " ")) title <- gsub(" +", " ", paste0(title, collapse = " "))
x <- plot_prepare_table(data, expand = expand) x <- plot_prepare_table(data, expand = expand)
cols_sub <- plot_colours_and_sub(x = x, cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo, mo = mo,
ab = ab, ab = ab,
guideline = guideline, guideline = guideline,
colours_RSI = colours_RSI, colours_RSI = colours_RSI,
fn = as.mic, fn = as.mic,
...) ...)
df <- as.data.frame(x, stringsAsFactors = TRUE) df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("mic", "count") colnames(df) <- c("mic", "count")
df$cols <- cols_sub$cols df$cols <- cols_sub$cols
df$cols[df$cols == colours_RSI[1]] <- "Resistant" df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible" df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- "Incr. exposure" df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols <- factor(df$cols, df$cols <- factor(df$cols,
levels = c("Susceptible", "Incr. exposure", "Resistant"), levels = c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
ordered = TRUE) ordered = TRUE)
if (!is.null(mapping)) { if (!is.null(mapping)) {
p <- ggplot2::ggplot(df, mapping = mapping) p <- ggplot2::ggplot(df, mapping = mapping)
@ -218,10 +221,11 @@ ggplot.mic <- function(data,
if (any(colours_RSI %in% cols_sub$cols)) { if (any(colours_RSI %in% cols_sub$cols)) {
p <- p + p <- p +
ggplot2::geom_col(aes(x = mic, y = count, fill = cols)) + ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
ggplot2::scale_fill_manual(values = c("Resistant" = colours_RSI[1], ggplot2::scale_fill_manual(values = c("Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2], "Susceptible" = colours_RSI[2],
"Incr. exposure" = colours_RSI[3]),, "Incr. exposure" = colours_RSI[3],
"Intermediate" = colours_RSI[3]),
name = NULL) name = NULL)
} else { } else {
p <- p + p <- p +
@ -235,7 +239,7 @@ ggplot.mic <- function(data,
#' @method plot disk #' @method plot disk
#' @export #' @export
#' @importFrom graphics barplot axis mtext #' @importFrom graphics barplot axis mtext legend
#' @rdname plot #' @rdname plot
plot.disk <- function(x, plot.disk <- function(x,
main = paste("Disk zones values of", deparse(substitute(x))), main = paste("Disk zones values of", deparse(substitute(x))),
@ -261,13 +265,13 @@ plot.disk <- function(x,
x <- plot_prepare_table(x, expand = expand) x <- plot_prepare_table(x, expand = expand)
cols_sub <- plot_colours_and_sub(x = x, cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo, mo = mo,
ab = ab, ab = ab,
guideline = guideline, guideline = guideline,
colours_RSI = colours_RSI, colours_RSI = colours_RSI,
fn = as.disk, fn = as.disk,
...) ...)
barplot(x, barplot(x,
col = cols_sub$cols, col = cols_sub$cols,
@ -289,7 +293,7 @@ plot.disk <- function(x,
legend_col <- colours_RSI[1] legend_col <- colours_RSI[1]
} }
if (colours_RSI[3] %in% cols_sub$cols) { if (colours_RSI[3] %in% cols_sub$cols) {
legend_txt <- c(legend_txt, "Incr. exposure") legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3]) legend_col <- c(legend_col, colours_RSI[3])
} }
if (colours_RSI[2] %in% cols_sub$cols) { if (colours_RSI[2] %in% cols_sub$cols) {
@ -367,21 +371,21 @@ ggplot.disk <- function(data,
title <- gsub(" +", " ", paste0(title, collapse = " ")) title <- gsub(" +", " ", paste0(title, collapse = " "))
x <- plot_prepare_table(data, expand = expand) x <- plot_prepare_table(data, expand = expand)
cols_sub <- plot_colours_and_sub(x = x, cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo, mo = mo,
ab = ab, ab = ab,
guideline = guideline, guideline = guideline,
colours_RSI = colours_RSI, colours_RSI = colours_RSI,
fn = as.disk, fn = as.disk,
...) ...)
df <- as.data.frame(x, stringsAsFactors = TRUE) df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("disk", "count") colnames(df) <- c("disk", "count")
df$cols <- cols_sub$cols df$cols <- cols_sub$cols
df$cols[df$cols == colours_RSI[1]] <- "Resistant" df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible" df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- "Incr. exposure" df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols <- factor(df$cols, df$cols <- factor(df$cols,
levels = c("Resistant", "Incr. exposure", "Susceptible"), levels = c("Resistant", plot_name_of_I(cols_sub$guideline), "Susceptible"),
ordered = TRUE) ordered = TRUE)
if (!is.null(mapping)) { if (!is.null(mapping)) {
p <- ggplot2::ggplot(df, mapping = mapping) p <- ggplot2::ggplot(df, mapping = mapping)
@ -394,7 +398,8 @@ ggplot.disk <- function(data,
ggplot2::geom_col(aes(x = disk, y = count, fill = cols)) + ggplot2::geom_col(aes(x = disk, y = count, fill = cols)) +
ggplot2::scale_fill_manual(values = c("Resistant" = colours_RSI[1], ggplot2::scale_fill_manual(values = c("Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2], "Susceptible" = colours_RSI[2],
"Incr. exposure" = colours_RSI[3]), "Incr. exposure" = colours_RSI[3],
"Intermediate" = colours_RSI[3]),
name = NULL) name = NULL)
} else { } else {
p <- p + p <- p +
@ -402,7 +407,7 @@ ggplot.disk <- function(data,
} }
p + p +
ggplot2::labs(title = title, x = xlab, y = ylab, sub = cols_sub$sub) ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
} }
plot_prepare_table <- function(x, expand) { plot_prepare_table <- function(x, expand) {
@ -413,7 +418,9 @@ plot_prepare_table <- function(x, expand) {
while (min(extra_range) / 2 > min(as.double(x))) { while (min(extra_range) / 2 > min(as.double(x))) {
extra_range <- c(min(extra_range) / 2, extra_range) extra_range <- c(min(extra_range) / 2, extra_range)
} }
extra_range <- setNames(rep(0, length(extra_range)), extra_range) nms <- extra_range
extra_range <- rep(0, length(extra_range))
names(extra_range) <- nms
x <- table(droplevels(x, as.mic = FALSE)) x <- table(droplevels(x, as.mic = FALSE))
extra_range <- extra_range[!names(extra_range) %in% names(x)] extra_range <- extra_range[!names(extra_range) %in% names(x)]
x <- as.table(c(x, extra_range)) x <- as.table(c(x, extra_range))
@ -437,12 +444,22 @@ plot_prepare_table <- function(x, expand) {
as.table(x) as.table(x)
} }
plot_colours_and_sub <- function(x, mo, ab, guideline, colours_RSI, fn, ...) { plot_name_of_I <- function(guideline) {
if (!guideline %like% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
# interpretation since 2019
"Incr. exposure"
} else {
# interpretation until 2019
"Intermediate"
}
}
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, ...) {
guideline <- get_guideline(guideline, AMR::rsi_translation)
if (!is.null(mo) && !is.null(ab)) { if (!is.null(mo) && !is.null(ab)) {
# interpret and give colour based on MIC values # interpret and give colour based on MIC values
mo <- as.mo(mo) mo <- as.mo(mo)
ab <- as.ab(ab) ab <- as.ab(ab)
guideline <- get_guideline(guideline, AMR::rsi_translation)
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...))) rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
cols <- character(length = length(rsi)) cols <- character(length = length(rsi))
cols[is.na(rsi)] <- "#BEBEBE" cols[is.na(rsi)] <- "#BEBEBE"
@ -454,16 +471,16 @@ plot_colours_and_sub <- function(x, mo, ab, guideline, colours_RSI, fn, ...) {
if (all(cols == "#BEBEBE")) { if (all(cols == "#BEBEBE")) {
message_("No ", guideline, " interpretations found for ", message_("No ", guideline, " interpretations found for ",
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname) ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
guideline <- "" guideline_txt <- ""
} else { } else {
guideline <- paste0("(following ", guideline, ")") guideline_txt <- paste0("(following ", guideline, ")")
} }
sub <- bquote(.(abname)~"in"~italic(.(moname))~.(guideline)) sub <- bquote(.(abname)~"in"~italic(.(moname))~.(guideline_txt))
} else { } else {
cols <- "#BEBEBE" cols <- "#BEBEBE"
sub <- NULL sub <- NULL
} }
list(cols = cols, sub = sub) list(cols = cols, sub = sub, guideline = guideline)
} }

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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

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2
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

16
docs/extra.css
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@ -187,30 +187,30 @@ div[id^=last-updated] h2 {
} }
/* tables, make them look like scientific ones */ /* tables, make them look like scientific ones */
table { .table {
font-size: 90%; font-size: 90%;
} }
table * { .table * {
vertical-align: middle !important; vertical-align: middle !important;
} }
table td { .table td {
padding: 4px !important; padding: 4px !important;
} }
thead { .table thead {
border-top: 2px solid black; border-top: 2px solid black;
border-bottom: 2px solid black; border-bottom: 2px solid black;
} }
thead ~ tbody { .table thead ~ tbody {
/* only when it has a header */ /* only when it has a header */
border-bottom: 2px solid black; border-bottom: 2px solid black;
} }
thead th { .table thead th {
text-align: inherit; text-align: inherit;
} }
table a:not(.btn), .table a:not(.btn) { .table a:not(.btn) {
text-decoration: inherit; text-decoration: inherit;
} }
table a:not(.btn):hover, .table a:not(.btn):hover { .table a:not(.btn):hover {
text-decoration: underline; text-decoration: underline;
} }

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

48
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1509025" class="section level1"> <div id="amr-1509026" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9025"> <h1 class="page-header" data-toc-text="1.5.0.9026">
<a href="#amr-1509025" class="anchor"></a>AMR 1.5.0.9025<small> Unreleased </small> <a href="#amr-1509026" class="anchor"></a>AMR 1.5.0.9026<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-25-february-2021" class="section level2"> <div id="last-updated-25-february-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -333,6 +333,8 @@
<em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li> <em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li>
<li> <li>
<code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_mic()</a></code> now have an expanded range in their randomisation</li> <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_mic()</a></code> now have an expanded range in their randomisation</li>
<li>Support for GISA (glycopeptide-intermediate <em>S. aureus</em>), so e.g. <code><a href="../reference/mo_property.html">mo_genus("GISA")</a></code> will return <code>"Staphylococcus"</code>
</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">
@ -659,7 +661,7 @@
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p> <p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p> <p>Negative effects of this change are:</p>
<ul> <ul>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li> <li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li> <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li> <li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li> <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@ -996,7 +998,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div> <span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p> <p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
</li> </li>
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li> <li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li> <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul> </ul>
</div> </div>
@ -1265,7 +1267,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li> <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code> <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
</li> </li>
<li>Frequency tables (<code>freq()</code>): <li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
<ul> <ul>
<li><p>speed improvement for microbial IDs</p></li> <li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li> <li><p>fixed factor level names for R Markdown</p></li>
@ -1275,12 +1277,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"> <code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># grouped boxplots:</span> <span class="co"># grouped boxplots:</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div> <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</li> </li>
</ul> </ul>
@ -1290,7 +1292,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em> <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li> </li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li> <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code> <li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
</li> </li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li> <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -1531,7 +1533,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li> </li>
</ul> </ul>
</li> </li>
<li>Frequency tables (<code>freq()</code> function): <li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
<ul> <ul>
<li> <li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p> <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@ -1541,15 +1543,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co"># OLD WAY</span> <span class="co"># OLD WAY</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
<span class="co"># NEW WAY</span> <span class="co"># NEW WAY</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
<span class="co"># Even supports grouping variables:</span> <span class="co"># Even supports grouping variables:</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
</li> </li>
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li> <li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li> <li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@ -1632,7 +1634,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li> <li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li> <li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
<li> <li>
<p>Frequency tables - <code>freq()</code>:</p> <p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
<ul> <ul>
<li> <li>
<p>Support for grouping variables, test with:</p> <p>Support for grouping variables, test with:</p>
@ -1640,14 +1642,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<code class="sourceCode R"> <code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
</li> </li>
<li> <li>
<p>Support for (un)selecting columns:</p> <p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
<code class="sourceCode R"> <code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
</li> </li>
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li> <li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@ -1665,7 +1667,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li> <li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li> <li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li> <li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li> <li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li> <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
<li> <li>
<p>AI improvements for <code>as.mo</code>:</p> <p>AI improvements for <code>as.mo</code>:</p>
@ -1833,13 +1835,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
<code class="sourceCode R"> <code class="sourceCode R">
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span> <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
<p>For lists, subsetting is possible:</p> <p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
<code class="sourceCode R"> <code class="sourceCode R">
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span> <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div> <span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
</li> </li>
</ul> </ul>
</div> </div>
@ -1913,13 +1915,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<li>A vignette to explain its usage</li> <li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li> <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code> <li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
</li> </li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code> <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li> </li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code> <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li> </li>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code> <li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li> </li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li> <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li> <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-02-25T09:21Z last_built: 2021-02-25T11:30Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

13
docs/reference/ggplot_rsi.html
View File

@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>
@ -256,8 +256,8 @@
minimum <span class='op'>=</span> <span class='fl'>30</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
nrow <span class='op'>=</span> <span class='cn'>NULL</span>, nrow <span class='op'>=</span> <span class='cn'>NULL</span>,
colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span> colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#3CAEA3"</span>, SI <span class='op'>=</span> <span class='st'>"#3CAEA3"</span>, I <span class='op'>=</span> <span class='st'>"#F6D55C"</span>, IR <span class='op'>=</span> <span class='st'>"#ED553B"</span>, R <span class='op'>=</span>
<span class='st'>"#ff6961"</span><span class='op'>)</span>, <span class='st'>"#ED553B"</span><span class='op'>)</span>,
datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>, datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>, datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>,
datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>, datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>,
@ -362,7 +362,7 @@
</tr> </tr>
<tr> <tr>
<th>colours</th> <th>colours</th>
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> for standard <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours. The default colours are colour-blind friendly.</p></td> <td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> for standard <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p></td>
</tr> </tr>
<tr> <tr>
<th>datalabels</th> <th>datalabels</th>
@ -484,11 +484,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span> <span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span>
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='co'># a shorter version which also adjusts data label colours:</span> <span class='co'># a shorter version which also adjusts data label colours:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

7
docs/reference/plot.html
View File

@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>
@ -313,7 +313,7 @@
<table class="ref-arguments"> <table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup> <colgroup><col class="name" /><col class="desc" /></colgroup>
<tr> <tr>
<th>x</th> <th>x, data</th>
<td><p>MIC values created with <code><a href='as.mic.html'>as.mic()</a></code> or disk diffusion values created with <code><a href='as.disk.html'>as.disk()</a></code></p></td> <td><p>MIC values created with <code><a href='as.mic.html'>as.mic()</a></code> or disk diffusion values created with <code><a href='as.disk.html'>as.disk()</a></code></p></td>
</tr> </tr>
<tr> <tr>
@ -359,7 +359,8 @@
<p>The <code>ggplot</code> functions return a <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p> <p>The <code>ggplot</code> functions return a <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p> <p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p> <p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2> <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9025</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9026</span>
</span> </span>
</div> </div>

11
man/ggplot_rsi.Rd
View File

@ -24,8 +24,8 @@ ggplot_rsi(
minimum = 30, minimum = 30,
language = get_locale(), language = get_locale(),
nrow = NULL, nrow = NULL,
colours = c(S = "#61a8ff", SI = "#61a8ff", I = "#61f7ff", IR = "#ff6961", R = colours = c(S = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R =
"#ff6961"), "#ED553B"),
datalabels = TRUE, datalabels = TRUE,
datalabels.size = 2.5, datalabels.size = 2.5,
datalabels.colour = "grey15", datalabels.colour = "grey15",
@ -100,7 +100,7 @@ labels_rsi_count(
\item{nrow}{(when using \code{facet}) number of rows} \item{nrow}{(when using \code{facet}) number of rows}
\item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} for standard \link[ggplot2:ggplot]{ggplot2} colours. The default colours are colour-blind friendly.} \item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} for standard \link[ggplot2:ggplot]{ggplot2} colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.}
\item{datalabels}{show datalabels using \code{\link[=labels_rsi_count]{labels_rsi_count()}}} \item{datalabels}{show datalabels using \code{\link[=labels_rsi_count]{labels_rsi_count()}}}
@ -208,11 +208,6 @@ example_isolates \%>\%
CIP) \%>\% CIP) \%>\%
ggplot_rsi(x = "age_group") ggplot_rsi(x = "age_group")
# for colourblind mode, use divergent colours from the viridis package:
example_isolates \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%
ggplot_rsi() +
scale_fill_viridis_d()
# a shorter version which also adjusts data label colours: # a shorter version which also adjusts data label colours:
example_isolates \%>\% example_isolates \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\% select(AMX, NIT, FOS, TMP, CIP) \%>\%

4
man/plot.Rd
View File

@ -72,7 +72,7 @@
) )
} }
\arguments{ \arguments{
\item{x}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}} \item{x, data}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}
\item{main, title}{title of the plot} \item{main, title}{title of the plot}
@ -99,6 +99,8 @@ The \code{ggplot} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model
Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base R and \code{ggplot2}. Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base R and \code{ggplot2}.
} }
\details{ \details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010". For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.

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@ -187,30 +187,30 @@ div[id^=last-updated] h2 {
} }
/* tables, make them look like scientific ones */ /* tables, make them look like scientific ones */
table { .table {
font-size: 90%; font-size: 90%;
} }
table * { .table * {
vertical-align: middle !important; vertical-align: middle !important;
} }
table td { .table td {
padding: 4px !important; padding: 4px !important;
} }
thead { .table thead {
border-top: 2px solid black; border-top: 2px solid black;
border-bottom: 2px solid black; border-bottom: 2px solid black;
} }
thead ~ tbody { .table thead ~ tbody {
/* only when it has a header */ /* only when it has a header */
border-bottom: 2px solid black; border-bottom: 2px solid black;
} }
thead th { .table thead th {
text-align: inherit; text-align: inherit;
} }
table a:not(.btn), .table a:not(.btn) { .table a:not(.btn) {
text-decoration: inherit; text-decoration: inherit;
} }
table a:not(.btn):hover, .table a:not(.btn):hover { .table a:not(.btn):hover {
text-decoration: underline; text-decoration: underline;
} }

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vignettes/AMR.Rmd
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@ -111,34 +111,26 @@ bacteria <- c("Escherichia coli", "Staphylococcus aureus",
"Streptococcus pneumoniae", "Klebsiella pneumoniae") "Streptococcus pneumoniae", "Klebsiella pneumoniae")
``` ```
## Other variables
For completeness, we can also add the hospital where the patients was admitted and we need to define valid antibmicrobial results for our randomisation:
```{r create other}
hospitals <- c("Hospital A", "Hospital B", "Hospital C", "Hospital D")
ab_interpretations <- c("S", "I", "R")
```
## Put everything together ## Put everything together
Using the `sample()` function, we can randomly select items from all objects we defined earlier. To let our fake data reflect reality a bit, we will also approximately define the probabilities of bacteria and the antibiotic results with the `prob` parameter. Using the `sample()` function, we can randomly select items from all objects we defined earlier. To let our fake data reflect reality a bit, we will also approximately define the probabilities of bacteria and the antibiotic results, using the `random_rsi()` function.
```{r merge data} ```{r merge data}
sample_size <- 20000 sample_size <- 20000
data <- data.frame(date = sample(dates, size = sample_size, replace = TRUE), data <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
patient_id = sample(patients, size = sample_size, replace = TRUE), patient_id = sample(patients, size = sample_size, replace = TRUE),
hospital = sample(hospitals, size = sample_size, replace = TRUE, hospital = sample(c("Hospital A",
"Hospital B",
"Hospital C",
"Hospital D"),
size = sample_size, replace = TRUE,
prob = c(0.30, 0.35, 0.15, 0.20)), prob = c(0.30, 0.35, 0.15, 0.20)),
bacteria = sample(bacteria, size = sample_size, replace = TRUE, bacteria = sample(bacteria, size = sample_size, replace = TRUE,
prob = c(0.50, 0.25, 0.15, 0.10)), prob = c(0.50, 0.25, 0.15, 0.10)),
AMX = sample(ab_interpretations, size = sample_size, replace = TRUE, AMX = random_rsi(sample_size, prob_RSI = c(0.35, 0.60, 0.05)),
prob = c(0.60, 0.05, 0.35)), AMC = random_rsi(sample_size, prob_RSI = c(0.15, 0.75, 0.10)),
AMC = sample(ab_interpretations, size = sample_size, replace = TRUE, CIP = random_rsi(sample_size, prob_RSI = c(0.20, 0.80, 0.00)),
prob = c(0.75, 0.10, 0.15)), GEN = random_rsi(sample_size, prob_RSI = c(0.08, 0.92, 0.00)))
CIP = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.80, 0.00, 0.20)),
GEN = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.92, 0.00, 0.08)))
``` ```
Using the `left_join()` function from the `dplyr` package, we can 'map' the gender to the patient ID using the `patients_table` object we created earlier: Using the `left_join()` function from the `dplyr` package, we can 'map' the gender to the patient ID using the `patients_table` object we created earlier:
@ -443,6 +435,7 @@ data_1st %>%
``` ```
## Plots ## Plots
To show results in plots, most R users would nowadays use the `ggplot2` package. This package lets you create plots in layers. You can read more about it [on their website](https://ggplot2.tidyverse.org/). A quick example would look like these syntaxes: To show results in plots, most R users would nowadays use the `ggplot2` package. This package lets you create plots in layers. You can read more about it [on their website](https://ggplot2.tidyverse.org/). A quick example would look like these syntaxes:
```{r plot 2, eval = FALSE} ```{r plot 2, eval = FALSE}
@ -480,7 +473,7 @@ ggplot(data_1st %>% group_by(genus)) +
geom_rsi(x = "genus") + geom_rsi(x = "genus") +
# split plots on antibiotic # split plots on antibiotic
facet_rsi(facet = "antibiotic") + facet_rsi(facet = "antibiotic") +
# set colours to the R/SI interpretations # set colours to the R/SI interpretations (colour-blind friendly)
scale_rsi_colours() + scale_rsi_colours() +
# show percentages on y axis # show percentages on y axis
scale_y_percent(breaks = 0:4 * 25) + scale_y_percent(breaks = 0:4 * 25) +
@ -506,6 +499,65 @@ data_1st %>%
coord_flip() coord_flip()
``` ```
### Plotting MIC and disk diffusion values
The AMR package also extends the `plot()` and `ggplot()` functions for plotting minimum inhibitory concentrations (MIC, created with `as.mic()`) and disk diffusion diameters (created with `as.disk()`).
With the `random_mic()` and `random_disk()` functions, we can generate sampled values for the new data types (S3 classes) `<mic>` and `<disk>`:
```{r, results='markup'}
mic_values <- random_mic(size = 100)
mic_values
```
```{r}
# base R:
plot(mic_values)
# ggplot2:
ggplot(mic_values)
```
But we could also be more specific, by generating MICs that are likely to be found in *E. coli* for ciprofloxacin:
```{r, results = 'markup', message = FALSE, warning = FALSE}
# this will generate MICs that are likely to be found in E. coli for ciprofloxacin:
mic_values_specific <- random_mic(size = 100, mo = "E. coli", ab = "cipro")
```
For the `plot()` and `ggplot()` function, we can define the microorganism and an antimicrobial agent the same way. This will add the interpretation of those values according to a chosen guidelines (defaults to the latest EUCAST guideline).
Default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red:
```{r, message = FALSE, warning = FALSE}
# base R:
plot(mic_values_specific, mo = "E. coli", ab = "cipro")
# ggplot2:
ggplot(mic_values_specific, mo = "E. coli", ab = "cipro")
```
For disk diffusion values, there is not much of a difference in plotting:
```{r, results = 'markup'}
# this will generate disks that are likely to be found in E. coli for ciprofloxacin:
disk_values_specific <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values_specific
```
```{r, message = FALSE, warning = FALSE}
# base R:
plot(disk_values_specific, mo = "E. coli", ab = "cipro")
```
And when using the `ggplot2` package, but now choosing the latest implemented CLSI guideline (notice that the EUCAST-specific term "Incr. exposure" has changed to "Intermediate"):
```{r, message = FALSE, warning = FALSE}
# and ggplot2, but now choosing an old CLSI guideline:
ggplot(disk_values_specific,
mo = "E. coli",
ab = "cipro",
guideline = "CLSI")
```
## Independence test ## Independence test
The next example uses the `example_isolates` data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis. The next example uses the `example_isolates` data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.