#' @title Incidence and lethality rate by region of COVID19
#' @aliases g_incidence_region
#' @description This function graphs the incidence and lethality by region of the COVID19 in the DR.
#' @usage g_incidence_region(saveplot = FALSE, savepng = FALSE)
#' @param saveplot Logical. Should save the ggplot objet to the \code{.GlobalEnv}? Default \code{FALSE}.
#' @param savepng Logical. Should save a png version of the plot? Default \code{FALSE}.
#' @return Graph of incidence and case fatality by region and save a
#' copy in png format to the computer at the address defined in \code{setwd()}.
#' @importFrom scales comma
#' @export
#' @examples
#' g_incidence_region()
#' g_incidence_region(saveplot = FALSE, savepng = TRUE)
#' @name g_incidence_region
g_incidence_region <- function(saveplot = FALSE,
savepng = FALSE){
if (exists('data_province') == FALSE) {
stop("data objects are missing, run load_data_covid_dr()")
}
df_inc <-
data_province %>%
filter(date == max(date)) %>%
left_join(
y = data_density %>%
select(Province, Pop),
by = "Province")
df_inc %<>%
mutate(Let = 100 * Deaths / Cases,
Incidence = Cases * 100000 / Pop,
Reg = case_when(Province %in% Metropolitan ~ 'Metropolitan',
Province %in% North ~ 'North',
Province %in% South ~ 'South',
Province %in% East ~ 'East',
Province %in% NE ~ 'NOESP')) %>%
filter(Cases != 0) %>%
drop_na(Incidence)
heatcol_inc <- sequential_hcl(n = 32,
palette = "YlOrRd",
power = 0.5,
l = 30,
c = 225,
c1 = 150)
heatcol_inc_reg <-
c('#0b559e', #azul
'#b50012', #rojo
'#03996f', #verde
'#805511') #marron
rep_actual <- data_cum$Reports %>% max(na.rm = TRUE)
max_inc_reg <-
df_inc %>%
summarise(max_inc = max(Incidence, na.rm = TRUE)) %>%
as.numeric() %>%
round(digits = -1) %>%
sum(15)
max_let_reg <-
df_inc %>%
summarise(max_inc = max(Let, na.rm = TRUE)) %>%
as.numeric() %>%
round(digits = -1) %>%
sum(10)
lab_inclet_reg <-
labs(title = "DR: COVID19 incidence and lethality by region and province",
subtitle = paste0('Incidence = Positive cases per 100,000 inhabitants',
' / Let = 100 * Deaths / Positive Cases'),
caption = paste0("Source: @fidelmorla with information from special bulletin #",
rep_actual,
" of @SaludPublicaRD y population reports of @ONERD_"),
x = "Let",
y = 'Incidence'
)
suppressWarnings(
g_inclet_reg <-
df_inc %>%
filter(!is.na(Reg)) %>%
ggplot(aes(x = Let,
y = Incidence,
color = as.factor(Reg),
size = Let,
fill = as.factor(Reg))) +
geom_jitter() +
scale_color_manual(values = heatcol_inc_reg) +
scale_fill_manual(values = heatcol_inc_reg) +
scale_y_continuous(labels = scales::comma,
breaks = c(seq(0,max_inc_reg, max_inc_reg/ 5)),
limits = c(-5,max_inc_reg)) +
facet_rep_wrap(. ~ fct_inorder(Reg),
ncol = 2,
repeat.tick.labels = 'all', scales = "fixed") +
geom_text_repel(show.legend = FALSE,
aes(size = 12,
label = case_when(Let > 10 ~ Province,
Incidence > 100 ~ Province)),
hjust = 0.2,
vjust = 1.2 ) +
lab_inclet_reg +
drcovidplots::list_themes['t6'] +
theme(axis.text.x = element_text(angle = 0),
strip.text.x = element_text(color = "white",
face = "bold.italic"),
strip.text.y = element_text(color = "white",
face = "bold.italic"),
strip.background = element_rect(color = "white",
fill = "#520041",
size = 0.1,
linetype = "solid")
)
)
print(g_inclet_reg) %>% suppressWarnings()
if (saveplot == TRUE) {assign('g_inclet_reg', g_inclet_reg, envir = .GlobalEnv)}
if (savepng == TRUE) {
ggsave(filename = "inclet_reg.png",
plot = g_inclet_reg,
device = "png",
width = 18.333333333333332 / 1.5,
height = 10.466666666666667 / 1.5,
units = "in")
}
}
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