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unit test fix

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dr. M.S. (Matthijs) Berends
2024-05-20 18:58:35 +02:00
parent 08a27922a8
commit fc269e667d
7 changed files with 17 additions and 12 deletions
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14
R/bug_drug_combinations.R
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@ -108,6 +108,7 @@ bug_drug_combinations <- function(x,
SDD = integer(0),
I = integer(0),
R = integer(0),
N = integer(0),
total = integer(0),
stringsAsFactors = FALSE
)
@ -122,18 +123,19 @@ bug_drug_combinations <- function(x,
x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.sir))), drop = FALSE]
# turn and merge everything
pivot <- lapply(x_mo_filter, function(x) {
m <- as.matrix(table(x))
data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
m <- as.matrix(table(as.sir(x)))
data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], N = m["N", ], stringsAsFactors = FALSE)
})
merged <- do.call(rbind_AMR, pivot)
out_group <- data.frame(
mo = rep(unique_mo[i], NROW(merged)),
ab = rownames(merged),
S = merged$S,
SDD = merged$SSD,
SDD = merged$SDD,
I = merged$I,
R = merged$R,
total = merged$S + merged$I + merged$R,
N = merged$N,
total = merged$S + merged$SDD + merged$I + merged$R + merged$N,
stringsAsFactors = FALSE
)
if (data_has_groups) {
@ -208,11 +210,13 @@ format.bug_drug_combinations <- function(x,
SDD = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$SDD[i], na.rm = TRUE)),
I = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$I[i], na.rm = TRUE)),
R = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
N = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
total = vapply(FUN.VALUE = double(1), idx, function(i) {
sum(x$S[i], na.rm = TRUE) +
sum(x$SDD[i], na.rm = TRUE) +
sum(x$I[i], na.rm = TRUE) +
sum(x$R[i], na.rm = TRUE)
sum(x$R[i], na.rm = TRUE) +
sum(x$N[i], na.rm = TRUE)
}),
stringsAsFactors = FALSE
)