#' Creates data dir for proessing
#' @author kenarab
#' @export
createDataDir <- function(){
download.flag <- TRUE
env.data.dir <- getEnv("data_dir")
if (!dir.exists(env.data.dir)){
prompt.value <- readline(prompt = paste("Just to create dir ", env.data.dir, ". Agree [y/n]?:", sep = ""))
if (tolower(prompt.value) %in% c("y", "yes")){
dir.create(env.data.dir, showWarnings = FALSE, recursive = TRUE)
}
else{
download.flag <- FALSE
}
}
download.flag
}
#' For copying generated graph to package folder
#' @author kenarab
#' @noRd
#' @export
copyPNG2package <- function(current.date = Sys.Date()){
env.data.dir <- getEnv("data_dir")
env.data.dir.files <- dir(env.data.dir)
env.data.dir.files <- env.data.dir.files[grep("\\.png", env.data.dir.files)]
env.data.dir.files <- env.data.dir.files[grep(as.character(current.date), env.data.dir.files)]
for (cf in env.data.dir.files){
dest.filename <- cf
dest.filename <- gsub(paste("-", current.date, sep = ""), "", dest.filename)
file.copy(file.path(env.data.dir, cf), file.path("inst/extdata/", dest.filename))
}
}
#' Diagnostic update situation of source repository
#' @author kenarab
#' @export
sourceRepoDiagnostic <- function(min.confirmed = 20){
data.processor <- COVID19DataProcessor$new(force.download = FALSE)
data.processor$curate()
all.countries <- data.processor$data %>% group_by(country) %>%
summarize(n = n(),
total.confirmed = max(confirmed))
all.countries$last.update <- vapply(all.countries$country,
FUN = function(x){
data.country <- data.processor$data[data.processor$data$country == x, ]
#ret <- data.country %>% filter(confirmed.inc > 0) %>% summarize(max.date = max(date))
data.country <- data.country %>% filter(imputation != "")
ret <- max(data.country$date)
ret <- as.character(ret)
ret
},
FUN.VALUE = character(1))
all.countries <- all.countries[all.countries$total.confirmed > min.confirmed, ]
repo.diagnostic <- all.countries %>%
group_by(last.update) %>%
summarize(n = n(), total.confirmed = sum(total.confirmed)) %>%
arrange(desc(last.update))
repo.diagnostic[, "countries (confirmed)"] <- vapply(repo.diagnostic$last.update,
FUN = function(x){
data.last.update <- all.countries[all.countries$last.update == x, ]
data.last.update <- data.last.update %>% arrange(desc(total.confirmed))
paste(data.last.update$country, "(", round(data.last.update$total.confirmed), ")", sep = "", collapse = ", ")
},
FUN.VALUE = character(1))
repo.diagnostic
}
#' genLogger
#' @author kenarab
#' @export
genLogger <- function(r6.object){
lgr::get_logger(class(r6.object)[[1]])
}
#' getLogger
#' @author kenarab
#' @export
getLogger <- function(r6.object){
ret <- r6.object$logger
if (is.null(ret)){
class <- class(r6.object)[[1]]
stop(paste("Class", class, "don't seems to have a configured logger"))
}
else{
ret.class <- class(ret)[[1]]
if (ret.class == "logical"){
stop(paste("Class", ret.class, "needs to initialize logger: self$logger <- genLogger(self)"))
}
}
ret
}
#' @description
#' kind of type checking
#' @author kenarab
#' @export
typeCheck <- function(object, class.name){
#TODO improve it using inherits
stopifnot(class(object)[[1]] == class.name)
}
#' @description
#' smooth a serie averaging last n values
#' @author kenarab
#' @import dplyr
#' @import zoo
#' @export
smoothSerie <- function(serie.name, serie, n){
n <- min(length(serie), n)
round(rollmeanr(serie, n, fill = NA))
}
#' @description
#' Countries object
#' @author kenarab
#' @import countrycode
#' @import dplyr
#' @export
Countries <- R6Class("Countries",
public = list(
#parameters
excluded.countries = c("Diamond Princess", "Kosovo"),
# state
data.processor = NA,
countries = NA,
countries.df = NA,
initialize = function(){
self
},
setup = function(countries){
self$countries <- as.character(countries)
countries.remove <- which(self$countries %in% self$excluded.countries)
countries.accepted <- self$countries
if (length(countries.remove) > 0){
countries.accepted <- self$countries[-countries.remove]
}
self$countries.df <- data.frame(country = countries.accepted,
continent = vapply(countries.accepted,
FUN = function(x)countrycode(x, origin = "country.name", destination = "continent"),
FUN.VALUE = character(1)),
stringsAsFactors = FALSE)
self$countries.df$sub.continent <- self$countries.df$continent
self$countries.df[self$countries.df$country %in% c("Argentina", "Bolivia", "Brazil", "Chile", "Colombia", "Ecuador", "French Guiana", "Guyana", "Paraguay", "Peru", "Suriname", "Uruguay", "Venezuela")
, "sub.continent"] <- "South America"
self$countries.df[self$countries.df$country %in% c("Costa Rica", "Guatemala", "Honduras", "Panama"), "sub.continent"] <- "Central America"
self$countries.df[self$countries.df$country %in% c("Antigua and Barbuda", "Aruba", "Cuba", "Dominican Republic", "Guadeloupe", "Jamaica", "Martinique", "Puerto Rico", "Saint Lucia", "Saint Vincent and the Grenadines", "The Bahamas", "Trinidad and Tobago"),
"sub.continent"] <- "Caribbean"
self$countries.df[self$countries.df$country %in% c("Canada", "Greenland", "Mexico", "US"),
"sub.continent"] <- "North America"
},
getCountries = function(division, name){
ret <- self$countries.df[self$countries.df[, division] %in% name, "country"]
ret
}
))
#' Get package directory
#'
#' Gets the path of package data.
#' @noRd
getPackageDir <- function(){
home.dir <- find.package("COVID19analytics", lib.loc = NULL, quiet = TRUE)
data.subdir <- file.path("inst", "extdata")
if (!dir.exists(file.path(home.dir, data.subdir)))
data.subdir <- "extdata"
file.path(home.dir, data.subdir)
}
#' getPackagePrefix
#' @author kenarab
#' @export
getPackagePrefix <- function(){
"COVID19analytics_"
}
#' getEnv
#' @author kenarab
#' @export
getEnv <- function(variable.name, package.prefix = getPackagePrefix(),
fail.on.empty = TRUE, env.file = "~/.Renviron", call.counter = 0){
prefixed.variable.name <- paste(package.prefix, variable.name, sep ="")
ret <- Sys.getenv(prefixed.variable.name)
if (nchar(ret) == 0){
if (call.counter == 0){
readRenviron(env.file)
ret <- getEnv(variable.name = variable.name, package.prefix = package.prefix,
fail.on.empty = fail.on.empty, env.file = env.file,
call.counter = call.counter + 1)
}
else{
if (fail.on.empty){
stop(paste("Must configure variable", prefixed.variable.name, " in", env.file))
}
}
}
ret
}
#' generateSticker
#' @import ggpubr
#' @noRd
generateSticker <- function(){
#library(hexSticker)
data.processor <- COVID19DataProcessor$new(provider = "JohnsHopkingsUniversity", missing.values = "imputation")
dummy <- data.processor$setupData()
dummy <- data.processor$transform()
dummy <- data.processor$curate()
top.countries <- data.processor$top.countries
international.countries <- unique(c(data.processor$top.countries[1:7],
"Japan", "Singapore", "Korea, South", "China"))
data.processor$data.comparison$data.compared$remaining.confirmed
field <- "remaining.confirmed"
data.long <- data.processor$data.comparison$data.compared %>%
select_at(c("country", "epidemy.day", field)) %>%
gather(key = type, value = count, -c(country, epidemy.day))
## set factor levels to show them in a desirable order
data.long %<>% mutate(type = factor(type, c(field)))
## cases by type
unique(df$country)
df <- data.long %>%
filter(count >= 100) %>%
filter(!country %in% "China" | epidemy.day < 108) %>%
mutate(country = fct_reorder(country, desc(count)))
df.all <- df %>% filter(epidemy.day >=0 & count >= 100)
unique(df.all$country)
df <- df %>% filter(country %in% international.countries)
p <- df %>% filter(country != "World") %>%
ggplot(aes(x = epidemy.day, y = count, color = country)) +
geom_line(data = df.all, aes(x = epidemy.day, y = count,
group = country, colour = "aaaa"), size = 0.2, show.legend = FALSE) +
geom_point(size = .005, show.legend = FALSE) +
scale_color_manual(values = c(gray = "gray",brewer.pal(n = 9, name = "Set1"),
brewer.pal(n = 8, name = "Set2"),
brewer.pal(n = 12, name = "Set3")),
) +
# scale_y_log10(labels = comma)
scale_y_log10(labels = NULL)
p <- p + theme_void() + theme_transparent()
sticker(p, package = "COVID19analytics",
p_color = brewer.pal(n = 11, name = "PiYG")[11],
p_size = 5, p_y = 0.6,
#p_family = "Courier new",
s_x= 1, s_y= 1.05, s_width=1.3, s_height=1.4,
#h_fill = "white",
h_fill = brewer.pal(n = 7, name = "PiYG")[5],
url = "https://github.com/rOpenStats/COVID19analytics",
u_size = 1.04,
u_x = 0.19,
u_y = 1.47,
filename="man/figures/COVID19analytics.png")
}
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