1
0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 18:46:11 +01:00
AMR/data-raw/reproduction_of_rsi_translation.R
2022-10-05 09:12:22 +02:00

179 lines
8.4 KiB
R
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
# Run it with source("data-raw/reproduction_of_rsi_translation.R")
library(dplyr)
library(readr)
library(tidyr)
library(AMR)
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Codes to data-raw/WHONET/Codes
DRGLST <- read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
DRGLST1 <- read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"), show_col_types = FALSE)
ORGLIST <- read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
# create data set for generic rules (i.e., AB-specific but not MO-specific)
rsi_generic <- DRGLST %>%
filter(CLSI == "X" | EUCST == "X") %>%
select(ab = ANTIBIOTIC, disk_dose = POTENCY, matches("^(CLSI|EUCST)[0-9]")) %>%
mutate(
ab = as.ab(ab),
across(matches("(CLSI|EUCST)"), as.double)
) %>%
pivot_longer(-c(ab, disk_dose), names_to = "method") %>%
separate(method, into = c("guideline", "method"), sep = "_") %>%
mutate(method = ifelse(method %like% "D",
gsub("D", "DISK_", method, fixed = TRUE),
gsub("M", "MIC_", method, fixed = TRUE)
)) %>%
separate(method, into = c("method", "rsi"), sep = "_") %>%
# I is in the middle, so we only need R and S (saves data)
filter(rsi %in% c("R", "S")) %>%
pivot_wider(names_from = rsi, values_from = value) %>%
transmute(
guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", guideline)),
method,
site = NA_character_,
mo = as.mo("UNKNOWN"),
ab,
ref_tbl = "Generic rules",
disk_dose,
breakpoint_S = S,
breakpoint_R = R,
uti = FALSE
) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)), !is.na(mo), !is.na(ab))
rsi_generic
# create data set for AB-specific and MO-specific rules
rsi_specific <- DRGLST1 %>%
# only support guidelines for humans (for now)
filter(
HOST == "Human" & SITE_INF %unlike% "canine|feline",
# only CLSI and EUCAST
GUIDELINES %like% "(CLSI|EUCST)"
) %>%
# get microorganism names from another WHONET table
mutate(ORG_CODE = tolower(ORG_CODE)) %>%
left_join(ORGLIST %>%
transmute(
ORG_CODE = tolower(ORG),
SCT_TEXT = case_when(
is.na(SCT_TEXT) & is.na(ORGANISM) ~ ORG_CODE,
is.na(SCT_TEXT) ~ ORGANISM,
TRUE ~ SCT_TEXT
)
) %>%
# WHO for 'Generic'
bind_rows(tibble(ORG_CODE = "gen", SCT_TEXT = "Unknown")) %>%
# WHO for 'Enterobacterales'
bind_rows(tibble(ORG_CODE = "ebc", SCT_TEXT = "Enterobacterales"))) %>%
# still some manual cleaning required
filter(!SCT_TEXT %in% c("Anaerobic Actinomycetes")) %>%
transmute(
guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
method = toupper(TESTMETHOD),
site = SITE_INF,
mo = as.mo(SCT_TEXT),
ab = as.ab(WHON5_CODE),
ref_tbl = REF_TABLE,
disk_dose = POTENCY,
breakpoint_S = as.double(ifelse(method == "DISK", DISK_S, MIC_S)),
breakpoint_R = as.double(ifelse(method == "DISK", DISK_R, MIC_R)),
uti = site %like% "(UTI|urinary|urine)"
) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)), !is.na(mo), !is.na(ab))
rsi_specific
rsi_translation <- rsi_generic %>%
bind_rows(rsi_specific) %>%
# add the taxonomic rank index, used for sorting (so subspecies match first, order matches last)
mutate(
rank_index = case_when(
mo_rank(mo) %like% "(infra|sub)" ~ 1,
mo_rank(mo) == "species" ~ 2,
mo_rank(mo) == "genus" ~ 3,
mo_rank(mo) == "family" ~ 4,
mo_rank(mo) == "order" ~ 5,
TRUE ~ 6
),
.after = mo
) %>%
arrange(desc(guideline), ab, mo, method) %>%
distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
as.data.frame(stringsAsFactors = FALSE)
# disks MUST be 6-50 mm, so correct where that is wrong:
rsi_translation[which(rsi_translation$method == "DISK" &
(is.na(rsi_translation$breakpoint_S) | rsi_translation$breakpoint_S > 50)), "breakpoint_S"] <- 50
rsi_translation[which(rsi_translation$method == "DISK" &
(is.na(rsi_translation$breakpoint_R) | rsi_translation$breakpoint_R < 6)), "breakpoint_R"] <- 6
m <- unique(as.double(as.mic(levels(as.mic(1)))))
rsi_translation[which(rsi_translation$method == "MIC" &
is.na(rsi_translation$breakpoint_S)), "breakpoint_S"] <- min(m)
rsi_translation[which(rsi_translation$method == "MIC" &
is.na(rsi_translation$breakpoint_R)), "breakpoint_R"] <- max(m)
# WHONET has no >1024 but instead uses 1025, 513, etc, so raise these one higher valid MIC factor level:
rsi_translation[which(rsi_translation$breakpoint_R == 129), "breakpoint_R"] <- m[which(m == 128) + 1]
rsi_translation[which(rsi_translation$breakpoint_R == 257), "breakpoint_R"] <- m[which(m == 256) + 1]
rsi_translation[which(rsi_translation$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
# EUCAST 2021 guideline: S <= 8 and R > 8
# WHONET file: S <= 8 and R >= 16
# this will make an MIC of 12 I, which should be R, so:
eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
rsi_translation$method == "MIC" &
log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0 &
!is.na(rsi_translation$breakpoint_R))
old_R <- rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE]
old_S <- rsi_translation[eucast_mics, "breakpoint_S", drop = TRUE]
new_R <- 2^(log2(old_R) - 1)
new_R[new_R < old_S | is.na(as.mic(new_R))] <- old_S[new_R < old_S | is.na(as.mic(new_R))]
rsi_translation[eucast_mics, "breakpoint_R"] <- new_R
eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
rsi_translation$method == "DISK" &
rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0 &
!is.na(rsi_translation$breakpoint_R))
rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
rsi_translation$disk_dose <- gsub("", "-", rsi_translation$disk_dose, fixed = TRUE)
# save to package
usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
rm(rsi_translation)
devtools::load_all(".")