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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
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parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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18
R/atc_online.R
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@ -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]]
}