mirror of https://github.com/msberends/AMR
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
138 lines
7.4 KiB
138 lines
7.4 KiB
# ==================================================================== # |
|
# TITLE # |
|
# Antimicrobial Resistance (AMR) Data Analysis for R # |
|
# # |
|
# SOURCE # |
|
# https://github.com/msberends/AMR # |
|
# # |
|
# LICENCE # |
|
# (c) 2018-2022 Berends MS, Luz CF et al. # |
|
# 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! |
|
|
|
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 <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-")) |
|
DRGLST1 <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-")) |
|
ORGLIST <- readr::read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-")) |
|
|
|
# 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] |
|
|
|
# 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) |
|
rm(rsi_translation) |
|
devtools::load_all(".")
|
|
|