mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 15:26:12 +01:00
207 lines
10 KiB
R
207 lines
10 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
|
# #
|
|
# 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 more info: https://msberends.github.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
# Read and format data ----------------------------------------------------
|
|
|
|
library(tidyverse)
|
|
library(maps)
|
|
library(httr)
|
|
|
|
GET_df <- function(ip) {
|
|
ip <- paste0("https://ipinfo.io/", ip, "?token=", ipinfo_token)
|
|
result <- ip %>% GET()
|
|
stop_for_status(result)
|
|
result %>%
|
|
content(type = "text", encoding = "UTF-8") %>%
|
|
jsonlite::fromJSON(flatten = TRUE) %>%
|
|
as_tibble()
|
|
}
|
|
|
|
# get website analytics
|
|
source("data-raw/country_analysis_url_token.R")
|
|
url_json <- paste0(country_analysis_url,
|
|
"/index.php?&module=API&token_auth=",
|
|
country_analysis_token,
|
|
"&method=Live.getLastVisitsDetails&idSite=3&language=en&expanded=1&date=2018-01-01,2028-01-01&period=range&filter_limit=-1&format=JSON&segment=&translateColumnNames=1")
|
|
data_json <- jsonlite::read_json(url_json)
|
|
data <- tibble(
|
|
timestamp_server = as.POSIXct(sapply(data_json, function(x) x$serverTimestamp), origin = "1970-01-01"),
|
|
ipaddress = sapply(data_json, function(x) x$visitIp))
|
|
rm(data_json)
|
|
|
|
# add country data based on IP address and ipinfo.io API
|
|
unique_ip <- unique(data$ipaddress)
|
|
ip_tbl <- GET_df(unique_ip[1])
|
|
p <- AMR:::progress_estimated(n = length(unique_ip) - 1, min_time = 0)
|
|
for (i in 2:length(unique_ip)) {
|
|
p$tick()
|
|
ip_tbl <- ip_tbl %>%
|
|
bind_rows(GET_df(unique_ip[i]))
|
|
}
|
|
close(p)
|
|
|
|
ip_tbl.bak <- ip_tbl
|
|
|
|
# add long and lat
|
|
ip_tbl <- ip_tbl %>%
|
|
separate(loc, into = c("y", "x"), sep = ",", remove = FALSE, convert = TRUE)
|
|
|
|
# Plot world map ----------------------------------------------------------
|
|
|
|
countries_geometry <- sf::st_as_sf(map('world', plot = FALSE, fill = TRUE)) %>%
|
|
mutate(countries_code = countrycode::countrycode(ID,
|
|
origin = 'country.name',
|
|
destination = 'iso2c',
|
|
custom_match = c("Ascension Island" = "GB", # Great Britain
|
|
"Azores" = "PT", # Portugal
|
|
"Barbuda" = "GB", # Great Britain
|
|
"Bonaire" = "BQ", # Bonaire, Saint Eustatius and Saba
|
|
"Canary Islands" = "ES", # Spain
|
|
"Chagos Archipelago" = "MU", # Mauritius
|
|
"Grenadines" = "VC", # Saint Vincent and the Grenadines
|
|
"Heard Island" = "AU", # Australia
|
|
"Kosovo" = "XK",
|
|
"Madeira Islands" = "PT", # Portugal
|
|
"Micronesia" = "FM",
|
|
"Saba" = "BQ", # Bonaire, Saint Eustatius and Saba
|
|
"Saint Martin" = "MF",
|
|
"Siachen Glacier" = "IN", # India
|
|
"Sint Eustatius" = "BQ" # Bonaire, Saint Eustatius and Saba
|
|
)),
|
|
included = as.integer(countries_code %in% ip_tbl$country),
|
|
not_antarctica = as.integer(ID != "Antarctica"),
|
|
countries_name = ifelse(included == 1, as.character(ID), NA))
|
|
|
|
# add countries not in the list
|
|
countries_missing <- unique(ip_tbl$country[!ip_tbl$country %in% countries_geometry$countries_code])
|
|
for (i in seq_len(length(countries_missing))) {
|
|
countries_geometry <- countries_geometry %>%
|
|
rbind(countries_geometry %>%
|
|
filter(ID == "Netherlands") %>%
|
|
mutate(ID = countrycode::countrycode(countries_missing[i],
|
|
origin = 'iso2c',
|
|
destination = 'country.name'),
|
|
countries_code = countries_missing[i],
|
|
included = 1,
|
|
not_antarctica = 1,
|
|
countries_name = countrycode::countrycode(countries_missing[i],
|
|
origin = 'iso2c',
|
|
destination = 'country.name')))
|
|
}
|
|
|
|
# how many?
|
|
countries_geometry %>% filter(included == 1) %>% nrow()
|
|
|
|
countries_geometry$countries_name <- gsub("UK", "United Kingdom", countries_geometry$countries_name, fixed = TRUE)
|
|
countries_geometry$countries_name <- gsub("USA", "United States", countries_geometry$countries_name, fixed = TRUE)
|
|
|
|
countries_plot <- ggplot(countries_geometry) +
|
|
geom_sf(aes(fill = included, colour = not_antarctica),
|
|
size = 0.25,
|
|
show.legend = FALSE) +
|
|
theme_minimal() +
|
|
theme(panel.grid = element_blank(),
|
|
axis.title = element_blank(),
|
|
axis.text = element_blank()) +
|
|
scale_fill_gradient(low = "white", high = "#128f7645") +
|
|
# this makes the border Antarctica turn white (invisible):
|
|
scale_colour_gradient(low = "white", high = "#128f76")
|
|
|
|
countries_plot_mini <- countries_plot
|
|
countries_plot_mini$data <- countries_plot_mini$data %>% filter(ID != "Antarctica")
|
|
# countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
|
|
countries_plot_big <- countries_plot +
|
|
labs(title = tools::toTitleCase("Countries the AMR package for R was downloaded from"),
|
|
subtitle = paste0("Between March 2018 (first release) and ",
|
|
format(Sys.Date(), "%B %Y")),
|
|
caption = "Source: https://cran-logs.rstudio.com") +
|
|
theme(plot.title = element_text(size = 16, hjust = 0.5),
|
|
plot.subtitle = element_text(size = 12, hjust = 0.5)) +
|
|
geom_text(aes(x = -170,
|
|
y = -75,
|
|
label = stringr::str_wrap(paste0("Countries (n = ",
|
|
length(countries_name[!is.na(countries_name)]), "): ",
|
|
paste(sort(countries_name[!is.na(countries_name)]), collapse = ", ")),
|
|
200)),
|
|
hjust = 0,
|
|
size = 4)
|
|
|
|
# main website page
|
|
ggsave("pkgdown/logos/countries.png",
|
|
width = 6,
|
|
height = 2.5,
|
|
units = "in",
|
|
dpi = 100,
|
|
plot = countries_plot_mini,
|
|
scale = 1)
|
|
# when clicked - a high res enlargement
|
|
ggsave("pkgdown/logos/countries_large.png",
|
|
width = 11,
|
|
height = 6,
|
|
units = "in",
|
|
dpi = 300,
|
|
plot = countries_plot_big,
|
|
scale = 1.5)
|
|
|
|
|
|
# Gibberish ---------------------------------------------------------------
|
|
|
|
data %>%
|
|
left_join(ip_tbl, by = c("ipaddress" = "ip")) %>%
|
|
group_by(country = countrycode::countrycode(country,
|
|
origin = 'iso2c',
|
|
destination = 'country.name',
|
|
custom_match = c(XK = "Kosovo"))) %>%
|
|
summarise(first = min(timestamp_server)) %>%
|
|
arrange(desc(first)) %>%
|
|
mutate(frame = case_when(first <= as.POSIXct("2019-06-30") ~ "Q1-Q2 2019",
|
|
first <= as.POSIXct("2019-12-31") ~ "Q3-Q4 2019",
|
|
TRUE ~ "Q1-Q2 2020")) %>%
|
|
View()
|
|
#
|
|
# p1 <- data %>%
|
|
# group_by(country) %>%
|
|
# summarise(first = min(timestamp_server)) %>%
|
|
# arrange(first) %>%
|
|
# mutate(n = row_number()) %>%
|
|
# ggplot(aes(x = first, y = n)) +
|
|
# geom_line() +
|
|
# geom_point(aes(x = max(first), y = max(n)), size = 3) +
|
|
# scale_x_datetime(date_breaks = "2 months", date_labels = "%B %Y") +
|
|
# labs(x = NULL, y = "Number of countries")
|
|
#
|
|
# package_releases <- read_html("https://cran.r-project.org/src/contrib/Archive/AMR/") %>%
|
|
# rvest::html_table() %>%
|
|
# .[[1]] %>%
|
|
# as_tibble(.name_repair = "unique") %>%
|
|
# filter(`Last modified` != "") %>%
|
|
# transmute(version = gsub("[^0-9.]", "",
|
|
# gsub(".tar.gz", "", Name)),
|
|
# datetime = as.POSIXct(`Last modified`)) %>%
|
|
# # add current
|
|
# bind_rows(tibble(version = as.character(packageVersion("AMR")),
|
|
# datetime = as.POSIXct(packageDate("AMR")))) %>%
|
|
# # remove the ones not plottable
|
|
# filter(datetime > min(p1$data$first))
|
|
#
|
|
# p1 + geom_linerange(data = package_releases, aes(x = datetime, ymin = 0, ymax = 80), colour = "red", inherit.aes = FALSE)
|
|
#
|