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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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12
R/random.R
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@ -91,10 +91,10 @@ random_sir <- function(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...) {
}
random_exec <- function(type, size, mo = NULL, ab = NULL) {
df <- clinical_breakpoints %pm>%
pm_filter(guideline %like% "EUCAST") %pm>%
pm_arrange(pm_desc(guideline)) %pm>%
subset(guideline == max(guideline) &
df <- clinical_breakpoints %>%
filter(guideline %like% "EUCAST") %>%
arrange(pm_desc(guideline)) %>%
filter(guideline == max(guideline) &
method == type)
if (!is.null(mo)) {
@ -105,7 +105,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
as.mo(mo_family(mo_coerced)),
as.mo(mo_order(mo_coerced))
)
df_new <- df %pm>%
df_new <- df %>%
subset(mo %in% mo_include)
if (nrow(df_new) > 0) {
df <- df_new
@ -116,7 +116,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
if (!is.null(ab)) {
ab_coerced <- as.ab(ab)
df_new <- df %pm>%
df_new <- df %>%
subset(ab %in% ab_coerced)
if (nrow(df_new) > 0) {
df <- df_new