Expected and actual deaths in Spain according to MoMo

MoMo_Spain.R

# Libraries ---------------------------------------------------------------

library(tidyverse)
library(data.table)


# Read data ---------------------------------------------------------------

# DOWNLOAD DATA FROM: https://momo.isciii.es/public/momo/dashboard/momo_dashboard.html#datos
DF_raw = read_csv("~/Downloads/data", guess_max = 10000)


# Parameters --------------------------------------------------------------

days_average = 7
filter_last_days = 5


# Data preparation --------------------------------------------------------

DF = DF_raw %>% 
  # Filters
  filter(ambito == "nacional") %>% 
  filter(cod_sexo == "all") %>% 
  filter(cod_gedad == "all") %>% 
  filter(fecha_defuncion < max(fecha_defuncion) - filter_last_days) %>%
  
  mutate(DIFF = defunciones_observadas - defunciones_esperadas) %>% 
  select(fecha_defuncion, defunciones_observadas, defunciones_esperadas, DIFF)


DF_plot = tibble(
  fecha_defuncion = DF$fecha_defuncion,
  defunciones_esperadas = frollmean(DF[, "defunciones_esperadas"], days_average) %>% unlist(),
  defunciones_observadas = frollmean(DF[, "defunciones_observadas"], days_average) %>% unlist()
) %>% 
  group_by(fecha_defuncion) %>% 
  summarise(defunciones_esperadas = sum(defunciones_esperadas, na.rm = FALSE),
            defunciones_observadas = sum(defunciones_observadas, na.rm = FALSE)) %>% 
  pivot_longer(2:3)
  
  

# Plot --------------------------------------------------------------------

  plot1 = ggplot(DF_plot, aes(fecha_defuncion, value, color = name)) +
    geom_line() +
    theme_minimal(base_size = 14) +
    scale_color_hue(l = 50) +
    scale_y_continuous(limits = c(600, max(DF_plot$value, na.rm = TRUE)), 
                       labels = seq(from = 600, to = max(DF_plot$value, na.rm = TRUE) + 100, by = 200),
                       breaks = seq(from = 600, to = max(DF_plot$value, na.rm = TRUE) + 100, by = 200)) +
    theme(legend.position = "bottom", legend.title = element_blank()) +
    labs(caption = paste0("Rolling average of last ", days_average, " days\n",
                          "Filtering out last ", filter_last_days, " days because of delayed reporting"))

  ggsave("NOT_GITHUB/DEV/plots/plot1.png", plot1, width = 16, height = 10)