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(v3.0.1.9002) replace WHONET directives with their GitHub repo

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dr. M.S. (Matthijs) Berends
2025-10-13 22:12:48 +02:00
parent 0b24967b23
commit d366949f1b
5 changed files with 24 additions and 21 deletions
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4
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR
Version: 3.0.1.9001
Date: 2025-09-30
Version: 3.0.1.9002
Date: 2025-10-13
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9001
# AMR 3.0.1.9002
### Changed
* Fixed a bug in `antibiogram()` for when no antimicrobials are set

18
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R
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@@ -35,24 +35,26 @@ library(readr)
library(tidyr)
devtools::load_all()
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
# (for ASIARS-Net update, also copy C:\WHONET\Codes to the data-raw/WHONET/ folder)
# BE SURE TO RUN data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R FIRST TO GET THE GROUPS!
# READ DATA ----
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
# files are retrieved from https://github.com/AClark-WHONET/AMRIE
github_repo <- "https://raw.github.com/AClark-WHONET/AMRIE/main/Interpretation%20Engine/Resources"
file_organisms <- file.path(github_repo, "Organisms.txt")
file_breakpoints <- file.path(github_repo, "Breakpoints.txt")
file_antibiotics <- file.path(github_repo, "Antibiotics.txt")
whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") |>
mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
show_col_types = FALSE, guess_max = Inf) |>
whonet_breakpoints <- read_tsv(file_breakpoints, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
filter(GUIDELINES %in% c("CLSI", "EUCAST"))
whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
whonet_antibiotics <- read_tsv(file_antibiotics, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
arrange(WHONET_ABX_CODE) |>
distinct(WHONET_ABX_CODE, .keep_all = TRUE)

19
data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R
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@@ -27,7 +27,7 @@
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().
# This data set is being referenced from in the clinical_breakpoints data set, and also by as.sir().
# It prevents the breakpoints table from being extremely long for species that are part of a species group.
# Also used by eucast_rules() to expand group names.
@@ -36,10 +36,6 @@ library(readr)
library(tidyr)
devtools::load_all()
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
# BACTERIAL COMPLEXES
# find all bacterial complex in the NCBI Taxonomy Browser here:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=6&lin=f&keep=1&srchmode=1&unlock
@@ -48,9 +44,14 @@ devtools::load_all()
# READ DATA ----
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
# files are retrieved from https://github.com/AClark-WHONET/AMRIE
github_repo <- "https://raw.github.com/AClark-WHONET/AMRIE/main/Interpretation%20Engine/Resources"
file_organisms <- file.path(github_repo, "Organisms.txt")
whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") %>%
filter(TAXONOMIC_STATUS == "C") |>
mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
whonet_organisms <- whonet_organisms %>%
@@ -87,7 +88,7 @@ microorganisms.groups <- whonet_organisms %>%
mo = ifelse(is.na(mo),
as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
mo)) %>%
# add our own CoNS and CoPS, WHONET does not strictly follow Becker et al (2014, 2019, 2020)
# add our own CoNS and CoPS, WHONET does not strictly follow Becker et al. (2014, 2019, 2020)
filter(mo_group != as.mo("CoNS")) %>%
bind_rows(tibble(mo_group = as.mo("CoNS"), mo = MO_CONS)) %>%
filter(mo_group != as.mo("CoPS")) %>%
@@ -153,7 +154,7 @@ microorganisms.groups <- whonet_organisms %>%
filter(mo_group != "B_YERSN_PSDT-C") %>%
bind_rows(tibble(mo_group = as.mo("B_YERSN_PSDT-C"),
mo = paste("Yersinia", c("pseudotuberculosis", "pestis", "similis", "wautersii")) %>% as.mo(keep_synonyms = TRUE))) %>%
# RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
# RGM are Rapidly-growing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
filter(mo_group != "B_MYCBC_RGM") %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE)))

2
pkgdown/extra.js
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@@ -145,7 +145,7 @@ $(function () {
x = x.replace("Kathryn", "Prof. Kathryn");
x = x.replace("Larisse", "Dr. Larisse");
x = x.replace("Matthijs", "Dr. Matthijs");
x = x.replace("Natacha", "Dr. Natacha");
x = x.replace("Natacha", "Prof. Natacha");
x = x.replace("Peter", "Dr. Peter");
x = x.replace("Rogier", "Dr. Rogier");
x = x.replace("Sofia", "Dr. Sofia");