mirror of https://github.com/msberends/AMR.git
(v1.5.0.9034) unit test fix
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Package: AMR
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Version: 1.5.0.9033
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Version: 1.5.0.9034
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Date: 2021-03-07
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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@ -48,6 +48,7 @@ S3method(as.data.frame,ab)
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S3method(as.data.frame,mo)
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S3method(as.double,mic)
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S3method(as.integer,mic)
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S3method(as.matrix,mic)
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S3method(as.numeric,mic)
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S3method(as.rsi,data.frame)
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S3method(as.rsi,default)
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@ -308,6 +309,7 @@ export(theme_rsi)
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importFrom(graphics,arrows)
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importFrom(graphics,axis)
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importFrom(graphics,barplot)
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importFrom(graphics,hist)
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importFrom(graphics,legend)
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importFrom(graphics,mtext)
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importFrom(graphics,plot)
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@ -316,8 +318,10 @@ importFrom(graphics,text)
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importFrom(stats,complete.cases)
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importFrom(stats,glm)
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importFrom(stats,lm)
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importFrom(stats,median)
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importFrom(stats,pchisq)
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importFrom(stats,prcomp)
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importFrom(stats,predict)
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importFrom(stats,qchisq)
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importFrom(stats,quantile)
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importFrom(stats,var)
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2
NEWS.md
2
NEWS.md
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@ -1,4 +1,4 @@
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# AMR 1.5.0.9033
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# AMR 1.5.0.9034
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## <small>Last updated: 7 March 2021</small>
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### New
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42
R/mic.R
42
R/mic.R
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@ -68,7 +68,7 @@
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#' #> 10 16 A
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#' ```
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#'
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#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log10()], [log1p()], [log2()], [max()], [mean()], [median()], [min()], [prod()], [quantile()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()].
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#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
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#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a numeric value.
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#' @aliases mic
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#' @export
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@ -118,29 +118,29 @@ as.mic <- function(x, na.rm = FALSE) {
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x <- gsub("\u2264", "<=", x, fixed = TRUE)
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x <- gsub("\u2265", ">=", x, fixed = TRUE)
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# remove space between operator and number ("<= 0.002" -> "<=0.002")
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x <- gsub("(<|=|>) +", "\\1", x)
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x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE)
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# transform => to >= and =< to <=
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x <- gsub("=<", "<=", x, fixed = TRUE)
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x <- gsub("=>", ">=", x, fixed = TRUE)
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# dots without a leading zero must start with 0
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x <- gsub("([^0-9]|^)[.]", "\\10.", x)
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x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
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# values like "<=0.2560.512" should be 0.512
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x <- gsub(".*[.].*[.]", "0.", x)
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x <- gsub(".*[.].*[.]", "0.", x, perl = TRUE)
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# remove ending .0
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x <- gsub("[.]+0$", "", x)
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x <- gsub("[.]+0$", "", x, perl = TRUE)
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# remove all after last digit
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x <- gsub("[^0-9]+$", "", x)
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x <- gsub("[^0-9]+$", "", x, perl = TRUE)
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# keep only one zero before dot
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x <- gsub("0+[.]", "0.", x)
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x <- gsub("0+[.]", "0.", x, perl = TRUE)
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# starting 00 is probably 0.0 if there's no dot yet
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x[!x %like% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
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# remove last zeroes
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x <- gsub("([.].?)0+$", "\\1", x)
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x <- gsub("(.*[.])0+$", "\\10", x)
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x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
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x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
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# remove ending .0 again
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x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
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# never end with dot
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x <- gsub("[.]$", "", x)
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x <- gsub("[.]$", "", x, perl = TRUE)
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# force to be character
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x <- as.character(x)
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# trim it
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@ -199,21 +199,21 @@ is.mic <- function(x) {
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#' @export
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#' @noRd
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as.double.mic <- function(x, ...) {
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as.double(gsub("[<=>]+", "", as.character(x)))
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as.double(gsub("[<=>]+", "", as.character(x), perl = TRUE))
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}
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#' @method as.integer mic
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#' @export
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#' @noRd
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as.integer.mic <- function(x, ...) {
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as.integer(gsub("[<=>]+", "", as.character(x)))
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as.integer(gsub("[<=>]+", "", as.character(x), perl = TRUE))
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}
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#' @method as.numeric mic
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#' @export
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#' @noRd
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as.numeric.mic <- function(x, ...) {
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as.numeric(gsub("[<=>]+", "", as.character(x)))
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as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
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}
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#' @method droplevels mic
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@ -263,6 +263,13 @@ summary.mic <- function(object, ...) {
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summary(as.double(object), ...)
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}
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#' @method as.matrix mic
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#' @export
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#' @noRd
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as.matrix.mic <- function(x, ...) {
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as.matrix(as.double(x), ...)
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}
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#' @method [ mic
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#' @export
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#' @noRd
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@ -328,10 +335,11 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
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}
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#' @method hist mic
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#' @importFrom graphics hist
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#' @export
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#' @noRd
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hist.mic <- function(x, ...) {
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warning_("Use `plot()` or `ggplot()` for plotting MIC values", call = FALSE)
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warning_("Use `plot()` or `ggplot()` for optimal plotting of MIC values", call = FALSE)
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hist(log2(x))
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}
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@ -357,18 +365,20 @@ mean.mic <- function(x, trim = 0, na.rm = FALSE, ...) {
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}
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#' @method median mic
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#' @importFrom stats median
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#' @export
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#' @noRd
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median.mic <- function(x, na.rm = FALSE, ...) {
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stats::median(as.double(x), na.rm = na.rm, ...)
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median(as.double(x), na.rm = na.rm, ...)
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}
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#' @method quantile mic
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#' @importFrom stats quantile
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#' @export
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#' @noRd
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quantile.mic <- function(x, probs = seq(0, 1, 0.25), na.rm = FALSE,
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names = TRUE, type = 7, ...) {
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stats::quantile(as.double(x), props = props, na.rm = na.rm, names = names, type = type, ...)
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quantile(as.double(x), probs = probs, na.rm = na.rm, names = names, type = type, ...)
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}
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# Math (see ?groupGeneric) ----------------------------------------------
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@ -121,10 +121,10 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
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}
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out <- as.mic(sample(set_range, size = size, replace = TRUE))
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# 50% chance that lowest will get <= and highest will get >=
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if (runif(1) > 0.5) {
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if (stats::runif(1) > 0.5) {
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out[out == min(out)] <- paste0("<=", out[out == min(out)])
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}
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if (runif(1) > 0.5) {
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if (stats::runif(1) > 0.5) {
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out[out == max(out)] <- paste0(">=", out[out == max(out)])
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}
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return(out)
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Binary file not shown.
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1509033" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9033">
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<a href="#amr-1509033" class="anchor"></a>AMR 1.5.0.9033<small> Unreleased </small>
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<div id="amr-1509034" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9034">
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<a href="#amr-1509034" class="anchor"></a>AMR 1.5.0.9034<small> Unreleased </small>
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</h1>
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<div id="last-updated-7-march-2021" class="section level2">
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<h2 class="hasAnchor">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-03-07T15:15Z
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last_built: 2021-03-07T19:41Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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File diff suppressed because one or more lines are too long
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9034</span>
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</span>
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</div>
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@ -54,7 +54,7 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
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#> 10 16 A
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}
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The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log10]{log10()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=median]{median()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}.
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The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
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}
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\section{Stable Lifecycle}{
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Reference in New Issue