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New mo algorithm, prepare for 2.0
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -232,7 +236,7 @@ ggplot_pca <- function(x,
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}
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# Overlay a concentration ellipse if there are groups
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if (!is.null(df.u$groups) & !is.null(ell) & isTRUE(ellipse)) {
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if (!is.null(df.u$groups) && !is.null(ell) && isTRUE(ellipse)) {
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g <- g + ggplot2::geom_path(
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data = ell,
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ggplot2::aes(colour = groups, group = groups),
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@ -319,7 +323,7 @@ pca_calculations <- function(pca_model,
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error = function(e) NULL
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)
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}
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if (!is.null(groups) & is.null(labels)) {
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if (!is.null(groups) && is.null(labels)) {
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# turn them around
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labels <- groups
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groups <- NULL
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