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(v1.5.0.9010) MDRO vignette update, get_episode for < day

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dr. M.S. (Matthijs) Berends
2021-01-24 14:48:56 +01:00
parent 1a88caa119
commit 286eaa9699
52 changed files with 319 additions and 210 deletions
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26
R/ggplot_pca.R
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@ -61,7 +61,7 @@
#' @rdname ggplot_pca
#' @export
#' @examples
#' # `example_isolates` is a dataset available in the AMR package.
#' # `example_isolates` is a data set available in the AMR package.
#' # See ?example_isolates.
#'
#' # See ?pca for more info about Principal Component Analysis (PCA).
@ -109,26 +109,26 @@ ggplot_pca <- function(x,
stop_ifnot_installed("ggplot2")
meet_criteria(x, allow_class = c("prcomp", "princomp", "PCA", "lda"))
meet_criteria(choices, allow_class = c("numeric", "integer"), has_length = 2)
meet_criteria(choices, allow_class = c("numeric", "integer"), has_length = 2, is_positive = TRUE, is_finite = TRUE)
meet_criteria(scale, allow_class = c("numeric", "integer", "logical"), has_length = 1)
meet_criteria(pc.biplot, allow_class = "logical", has_length = 1)
meet_criteria(labels, allow_class = "character", allow_NULL = TRUE)
meet_criteria(labels_textsize, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(labels_text_placement, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(labels_textsize, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(labels_text_placement, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(groups, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ellipse, allow_class = "logical", has_length = 1)
meet_criteria(ellipse_prob, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(ellipse_size, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(ellipse_alpha, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(points_size, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(points_alpha, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(ellipse_prob, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(ellipse_size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(ellipse_alpha, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(points_size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(points_alpha, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(arrows, allow_class = "logical", has_length = 1)
meet_criteria(arrows_colour, allow_class = "character", has_length = 1)
meet_criteria(arrows_size, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(arrows_textsize, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(arrows_size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(arrows_textsize, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(arrows_textangled, allow_class = "logical", has_length = 1)
meet_criteria(arrows_alpha, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(base_textsize, allow_class = c("numeric", "integer"), has_length = 1)
meet_criteria(arrows_alpha, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(base_textsize, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
calculations <- pca_calculations(pca_model = x,
groups = groups,