mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 10:21:56 +02:00
New mo algorithm, prepare for 2.0
This commit is contained in:
committed by
GitHub
parent
63fe160322
commit
cd2acc4a29
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# 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. #
|
||||
@ -94,9 +98,7 @@ atc_online_property <- function(atc_code,
|
||||
html_text <- import_fn("html_text", "rvest")
|
||||
read_html <- import_fn("read_html", "xml2")
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
if (!all(atc_code %in% unlist(antibiotics$atc))) {
|
||||
if (!all(atc_code %in% unlist(AMR::antibiotics$atc))) {
|
||||
atc_code <- as.character(ab_atc(atc_code, only_first = TRUE))
|
||||
}
|
||||
|
||||
@ -183,7 +185,7 @@ atc_online_property <- function(atc_code,
|
||||
# ATC and name are only in first row
|
||||
returnvalue[i] <- out[1, property, drop = TRUE]
|
||||
} else {
|
||||
if (!"adm.r" %in% colnames(out) | is.na(out[1, "adm.r", drop = TRUE])) {
|
||||
if (!"adm.r" %in% colnames(out) || is.na(out[1, "adm.r", drop = TRUE])) {
|
||||
returnvalue[i] <- NA
|
||||
next
|
||||
} else {
|
||||
@ -197,7 +199,7 @@ atc_online_property <- function(atc_code,
|
||||
}
|
||||
}
|
||||
|
||||
if (property == "groups" & length(returnvalue) == 1) {
|
||||
if (property == "groups" && length(returnvalue) == 1) {
|
||||
returnvalue <- returnvalue[[1]]
|
||||
}
|
||||
|
||||
|
Reference in New Issue
Block a user