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(v1.2.0.9034) code cleaning

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-07-13 09:17:24 +02:00
parent c0cf7ab02b
commit 6ab468362d
36 changed files with 266 additions and 265 deletions
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16
R/bug_drug_combinations.R
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@ -75,7 +75,7 @@ bug_drug_combinations <- function(x,
x <- x[, c(col_mo, names(which(sapply(x, is.rsi)))), drop = FALSE]
unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
out <- data.frame(
mo = character(0),
ab = character(0),
@ -83,7 +83,7 @@ bug_drug_combinations <- function(x,
I = integer(0),
R = integer(0),
total = integer(0))
for (i in seq_len(length(unique_mo))) {
# filter on MO group and only select R/SI columns
x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(sapply(x, is.rsi))), drop = FALSE]
@ -101,7 +101,7 @@ bug_drug_combinations <- function(x,
total = merged$S + merged$I + merged$R)
out <- rbind(out, out_group)
}
structure(.Data = out, class = c("bug_drug_combinations", x_class))
}
@ -172,11 +172,11 @@ format.bug_drug_combinations <- function(x,
y <- y %>%
create_var(txt = paste0(percentage(y$isolates / y$total, decimal.mark = decimal.mark, big.mark = big.mark),
" (", trimws(format(y$isolates, big.mark = big.mark)), "/",
trimws(format(y$total, big.mark = big.mark)), ")")) %>%
" (", trimws(format(y$isolates, big.mark = big.mark)), "/",
trimws(format(y$total, big.mark = big.mark)), ")")) %>%
select(ab, ab_txt, mo, txt) %>%
arrange(mo)
# replace tidyr::pivot_wider() from here
for (i in unique(y$mo)) {
mo_group <- y[which(y$mo == i), c("ab", "txt")]
@ -194,14 +194,14 @@ format.bug_drug_combinations <- function(x,
select_ab_vars <- function(.data) {
.data[, c("ab_group", "ab_txt", colnames(.data)[!colnames(.data) %in% c("ab_group", "ab_txt", "ab")])]
}
y <- y %>%
create_var(ab_group = ab_group(y$ab, language = language)) %>%
select_ab_vars() %>%
arrange(ab_group, ab_txt)
y <- y %>%
create_var(ab_group = ifelse(y$ab_group != lag(y$ab_group) | is.na(lag(y$ab_group)), y$ab_group, ""))
if (add_ab_group == FALSE) {
y <- y %>%
select(-ab_group) %>%