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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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R/pca.R
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@ -127,7 +127,7 @@ pca <- function(x,
x <- cbind(x.bak[, vapply(FUN.VALUE = logical(1), x.bak, function(y) !is.numeric(y) & !all(is.na(y))), drop = FALSE], x)
}
x <- pm_ungroup(x) # would otherwise select the grouping vars
x <- ungroup(x) # would otherwise select the grouping vars
x <- x[rowSums(is.na(x)) == 0, ] # remove columns containing NAs
pca_data <- x[, which(vapply(FUN.VALUE = logical(1), x, function(x) is.numeric(x))), drop = FALSE]