mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 16:42:10 +02:00
(v2.1.1.9242) sir log
This commit is contained in:
89
R/sir.R
89
R/sir.R
@ -111,7 +111,7 @@
|
||||
#'
|
||||
#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.sir(your_data)`.
|
||||
#'
|
||||
#' **For points 2, 3 and 4: Use [sir_interpretation_history()]** to retrieve a [data.frame] (or [tibble][tibble::tibble()] if the `tibble` package is installed) with all results of the last [as.sir()] call.
|
||||
#' **For points 2, 3 and 4: Use [sir_interpretation_history()]** to retrieve a [data.frame] with all results of all previous [as.sir()] calls. It also contains notes about interpretation, and the exact input and output values.
|
||||
#'
|
||||
#' ### Supported Guidelines
|
||||
#'
|
||||
@ -1506,30 +1506,29 @@ as_sir_method <- function(method_short,
|
||||
}
|
||||
|
||||
if (NROW(breakpoints_current) == 0) {
|
||||
AMR_env$sir_interpretation_history <- rbind_AMR(
|
||||
AMR_env$sir_interpretation_history,
|
||||
out <- data.frame(
|
||||
# recycling 1 to 2 rows does not always seem to work, which is why vectorise_log_entry() was added
|
||||
data.frame(
|
||||
datetime = vectorise_log_entry(Sys.time(), length(rows)),
|
||||
index = rows,
|
||||
method = vectorise_log_entry(method_coerced, length(rows)),
|
||||
ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
|
||||
mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
|
||||
host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
|
||||
input_given = vectorise_log_entry(as.character(values_bak), length(rows)),
|
||||
ab = vectorise_log_entry(ab_current, length(rows)),
|
||||
mo = vectorise_log_entry(mo_current, length(rows)),
|
||||
host = vectorise_log_entry(host_current, length(rows)),
|
||||
input = vectorise_log_entry(as.character(values), length(rows)),
|
||||
outcome = vectorise_log_entry(NA_sir_, length(rows)),
|
||||
notes = vectorise_log_entry("No breakpoint available", length(rows)),
|
||||
guideline = vectorise_log_entry(guideline_current, length(rows)),
|
||||
ref_table = vectorise_log_entry(NA_character_, length(rows)),
|
||||
uti = vectorise_log_entry(uti_current, length(rows)),
|
||||
breakpoint_S_R = vectorise_log_entry(NA_character_, length(rows)),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
datetime = vectorise_log_entry(Sys.time(), length(rows)),
|
||||
index = rows,
|
||||
method = vectorise_log_entry(method_coerced, length(rows)),
|
||||
ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
|
||||
mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
|
||||
host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
|
||||
input_given = vectorise_log_entry(as.character(values_bak), length(rows)),
|
||||
ab = vectorise_log_entry(ab_current, length(rows)),
|
||||
mo = vectorise_log_entry(mo_current, length(rows)),
|
||||
host = vectorise_log_entry(host_current, length(rows)),
|
||||
input = vectorise_log_entry(as.character(values), length(rows)),
|
||||
outcome = vectorise_log_entry(NA_sir_, length(rows)),
|
||||
notes = vectorise_log_entry("No breakpoint available", length(rows)),
|
||||
guideline = vectorise_log_entry(guideline_current, length(rows)),
|
||||
ref_table = vectorise_log_entry(NA_character_, length(rows)),
|
||||
uti = vectorise_log_entry(uti_current, length(rows)),
|
||||
breakpoint_S_R = vectorise_log_entry(NA_character_, length(rows)),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
out <- subset(out, !is.na(input_given))
|
||||
AMR_env$sir_interpretation_history <- rbind_AMR(AMR_env$sir_interpretation_history, out)
|
||||
notes <- c(notes, notes_current)
|
||||
next
|
||||
}
|
||||
@ -1636,6 +1635,7 @@ as_sir_method <- function(method_short,
|
||||
)
|
||||
}
|
||||
|
||||
## actual interpretation ----
|
||||
if (method == "mic") {
|
||||
new_sir <- case_when_AMR(
|
||||
is.na(values) ~ NA_sir_,
|
||||
@ -1668,30 +1668,29 @@ as_sir_method <- function(method_short,
|
||||
# write to verbose output
|
||||
notes_current <- trimws2(notes_current)
|
||||
notes_current[notes_current == ""] <- NA_character_
|
||||
AMR_env$sir_interpretation_history <- rbind_AMR(
|
||||
AMR_env$sir_interpretation_history,
|
||||
out <- data.frame(
|
||||
# recycling 1 to 2 rows does not always seem to work, which is why vectorise_log_entry() was added
|
||||
data.frame(
|
||||
datetime = vectorise_log_entry(Sys.time(), length(rows)),
|
||||
index = rows,
|
||||
method = vectorise_log_entry(method_coerced, length(rows)),
|
||||
ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
|
||||
mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
|
||||
host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
|
||||
input_given = vectorise_log_entry(as.character(values_bak), length(rows)),
|
||||
ab = vectorise_log_entry(breakpoints_current[, "ab", drop = TRUE], length(rows)),
|
||||
mo = vectorise_log_entry(breakpoints_current[, "mo", drop = TRUE], length(rows)),
|
||||
host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
|
||||
input = vectorise_log_entry(as.character(values), length(rows)),
|
||||
outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
|
||||
notes = font_stripstyle(notes_current), # vectorise_log_entry(paste0(font_stripstyle(notes_current), collapse = "\n"), length(rows)),
|
||||
guideline = vectorise_log_entry(guideline_current, length(rows)),
|
||||
ref_table = vectorise_log_entry(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
|
||||
uti = vectorise_log_entry(breakpoints_current[, "uti", drop = TRUE], length(rows)),
|
||||
breakpoint_S_R = vectorise_log_entry(paste0(breakpoints_current[, "breakpoint_S", drop = TRUE], "-", breakpoints_current[, "breakpoint_R", drop = TRUE]), length(rows)),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
datetime = vectorise_log_entry(Sys.time(), length(rows)),
|
||||
index = rows,
|
||||
method = vectorise_log_entry(method_coerced, length(rows)),
|
||||
ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
|
||||
mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
|
||||
host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
|
||||
input_given = vectorise_log_entry(as.character(values_bak), length(rows)),
|
||||
ab = vectorise_log_entry(breakpoints_current[, "ab", drop = TRUE], length(rows)),
|
||||
mo = vectorise_log_entry(breakpoints_current[, "mo", drop = TRUE], length(rows)),
|
||||
host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
|
||||
input = vectorise_log_entry(as.character(values), length(rows)),
|
||||
outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
|
||||
notes = font_stripstyle(notes_current), # vectorise_log_entry(paste0(font_stripstyle(notes_current), collapse = "\n"), length(rows)),
|
||||
guideline = vectorise_log_entry(guideline_current, length(rows)),
|
||||
ref_table = vectorise_log_entry(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
|
||||
uti = vectorise_log_entry(breakpoints_current[, "uti", drop = TRUE], length(rows)),
|
||||
breakpoint_S_R = vectorise_log_entry(paste0(breakpoints_current[, "breakpoint_S", drop = TRUE], "-", breakpoints_current[, "breakpoint_R", drop = TRUE]), length(rows)),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
out <- subset(out, !is.na(input_given))
|
||||
AMR_env$sir_interpretation_history <- rbind_AMR(AMR_env$sir_interpretation_history, out)
|
||||
}
|
||||
|
||||
notes <- c(notes, notes_current)
|
||||
|
||||
Reference in New Issue
Block a user