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mirror of https://github.com/msberends/AMR.git synced 2025-07-11 21:41:58 +02:00

(v1.1.0.9005) lose dependencies

This commit is contained in:
2020-05-16 20:08:21 +02:00
parent 7f3da74b17
commit df2456b91f
30 changed files with 342 additions and 736 deletions

View File

@ -83,8 +83,12 @@ atc_online_property <- function(atc_code,
if (!all(atc_code %in% antibiotics)) {
atc_code <- as.character(ab_atc(atc_code))
}
if (!curl::has_internet()) {
require("curl")
require("xml2")
require("rvest")
if (!has_internet()) {
message("There appears to be no internet connection.")
return(rep(NA, length(atc_code)))
}
@ -129,15 +133,15 @@ atc_online_property <- function(atc_code,
atc_url <- sub("%s", atc_code[i], url, fixed = TRUE)
if (property == "groups") {
tbl <- xml2::read_html(atc_url) %>%
rvest::html_node("#content") %>%
rvest::html_children() %>%
rvest::html_node("a")
tbl <- read_html(atc_url) %>%
html_node("#content") %>%
html_children() %>%
html_node("a")
# get URLS of items
hrefs <- tbl %>% rvest::html_attr("href")
hrefs <- tbl %>% html_attr("href")
# get text of items
texts <- tbl %>% rvest::html_text()
texts <- tbl %>% html_text()
# select only text items where URL like "code="
texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)]
# last one is antibiotics, skip it
@ -145,9 +149,9 @@ atc_online_property <- function(atc_code,
returnvalue <- c(list(texts), returnvalue)
} else {
tbl <- xml2::read_html(atc_url) %>%
rvest::html_nodes("table") %>%
rvest::html_table(header = TRUE) %>%
tbl <- read_html(atc_url) %>%
html_nodes("table") %>%
html_table(header = TRUE) %>%
as.data.frame(stringsAsFactors = FALSE)
# case insensitive column names