diff --git a/DESCRIPTION b/DESCRIPTION index 3d1510c4..06e74c81 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.5.0.9034 +Version: 1.5.0.9035 Date: 2021-03-07 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/R/ab.R b/R/ab.R index 655c53e2..2379b41c 100755 --- a/R/ab.R +++ b/R/ab.R @@ -105,7 +105,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) { already_regex <- isTRUE(list(...)$already_regex) fast_mode <- isTRUE(list(...)$fast_mode) - x_bak <- x x <- toupper(x) x_nonNA <- x[!is.na(x)] diff --git a/R/rsi.R b/R/rsi.R index 959d8797..8c7d8abb 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -774,6 +774,11 @@ exec_as.rsi <- function(method, for (i in seq_len(length(x))) { is_intrinsic_r <- paste(mo[i], ab) %in% INTRINSIC_R + if (is_intrinsic_r == TRUE) { + print("====") + print(paste(mo[i], ab)) + print("====") + } any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) { @@ -814,14 +819,22 @@ exec_as.rsi <- function(method, if (is.na(x[i])) { new_rsi[i] <- NA_character_ } else if (method == "mic") { + print("----") + print(str(get_record)) + print(x[i]) + print(x[i] <= get_record$breakpoint_S) + print(x[i] > get_record$breakpoint_R) + print(x[i] >= get_record$breakpoint_R) + print(guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R) + print(guideline_coerced %like% "EUCAST" && x[i] > get_record$breakpoint_R) + print(guideline_coerced %like% "EUCAST" & (x[i] > get_record$breakpoint_R)) + print("----") new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S", isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R", # start interpreting: EUCAST uses <= S and > R, CLSI uses <=S and >= R - isTRUE(x[i] <= get_record$breakpoint_S) ~ "S", - guideline_coerced %like% "EUCAST" & - isTRUE(x[i] > get_record$breakpoint_R) ~ "R", - guideline_coerced %like% "CLSI" & - isTRUE(x[i] >= get_record$breakpoint_R) ~ "R", + x[i] <= get_record$breakpoint_S ~ "S", + guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R ~ "R", + guideline_coerced %like% "CLSI" & x[i] >= get_record$breakpoint_R ~ "R", # return "I" when not match the bottom or top !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I", # and NA otherwise