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(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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7
R/sir_calc.R
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@@ -254,7 +254,6 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
if (message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
}
}
data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
}
@@ -359,12 +358,12 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
# don't use as.sir() here, as it would add the class 'sir' and we would like
# the same data structure as output, regardless of input
if (out$value[out$interpretation == "SDD"] > 0) {
out$interpretation <- factor(out$interpretation, levels = c("S", "SDD", "I", "R"), ordered = TRUE)
out$interpretation <- factor(out$interpretation, levels = c("S", "SDD", "I", "R"), ordered = TRUE)
} else {
out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)
}
}
out <- out[!is.na(out$interpretation), , drop = FALSE]
if (data_has_groups) {
@@ -383,6 +382,6 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
# remove redundant columns
out <- subset(out, select = -c(ci_min, ci_max, isolates))
}
as_original_data_class(out, class(data.bak), extra_class = "sir_df") # will remove tibble groups
}