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December 29, 2021 17:41
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COVID19 (Perú): Gráficos de positivos y fallecidos por semana epidemiológica
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# Inspirado en https://twitter.com/plenque/status/1475934854269259803 | |
library(tidyverse) | |
library(lubridate) | |
pos_url <- "https://github.com/jmcastagnetto/covid-19-peru-limpiar-datos-minsa/raw/main/datos/positivos_covid_aumentado.rds" | |
pos <- rio::import(pos_url) | |
pos_semana <- pos %>% | |
mutate( | |
sunday_of_week = floor_date( | |
fecha_resultado, | |
"weeks", | |
week_start = 7), | |
) %>% | |
group_by(epi_year, epi_week, sunday_of_week) %>% | |
tally(name = "positivos_semana") | |
fal_url <- "https://github.com/jmcastagnetto/covid-19-peru-limpiar-datos-minsa/raw/main/datos/fallecidos_covid_aumentado.rds" | |
fal <- rio::import(fal_url) | |
fal_semana <- fal %>% | |
mutate( | |
sunday_of_week = floor_date( | |
fecha_fallecimiento, | |
"weeks", | |
week_start = 7), | |
) %>% | |
group_by(epi_year, epi_week, sunday_of_week) %>% | |
tally(name = "fallecidos_semana") | |
comb <- pos_semana %>% | |
left_join( | |
fal_semana, | |
by = c("epi_year", "epi_week", "sunday_of_week") | |
) %>% | |
filter(!is.na(epi_year)) %>% | |
ungroup() %>% | |
filter(sunday_of_week < max(sunday_of_week)) %>% | |
mutate( | |
yw = as.numeric(sprintf("%4d%02d", epi_year, epi_week)), | |
yw_lbl = sprintf("%4d-S%02d", epi_year, epi_week) | |
) | |
factor <- round(max(comb$positivos_semana) / max(comb$fallecidos_semana), -1) | |
min_yw <- comb %>% | |
filter(yw == min(yw)) %>% | |
pull(yw_lbl) | |
max_yw <- comb %>% | |
filter(yw == max(yw)) %>% | |
pull(yw_lbl) | |
comb <- comb %>% | |
mutate( | |
fallecidos_semana_scaled = factor * fallecidos_semana | |
) | |
p1 <- ggplot(comb) + | |
geom_line(aes(x = sunday_of_week, y = positivos_semana), color = "blue") + | |
geom_line(aes(x = sunday_of_week, y = fallecidos_semana_scaled), color = "red") + | |
scale_y_continuous( | |
name = "Casos positivos", | |
labels = scales::comma, | |
sec.axis = sec_axis( | |
name = "Fallecidos", | |
trans = ~ . / factor, | |
labels = scales::comma | |
) | |
) + | |
scale_x_date( | |
name = "", | |
date_labels = "%b\n%Y", | |
date_breaks = "1 month" | |
) + | |
labs( | |
title = "COVID-19 (Perú): Casos positivos y fallecidos por semana epidemiológica", | |
subtitle = glue::glue("Fuente: Datos abiertos del MINSA, de {min_yw} a {max_yw}"), | |
caption = "@jmcastagnetto, Jesus M. Castagnetto" | |
) + | |
theme_minimal(16) + | |
theme( | |
plot.background = element_rect(fill = "white"), | |
axis.title.y.left = element_text(color = "blue", size = 18, face = "bold"), | |
axis.text.y.left = element_text(color = "blue"), | |
axis.title.y.right = element_text(color = "red", size = 18, face = "bold"), | |
axis.text.y.right = element_text(color = "red"), | |
plot.title.position = "plot", | |
plot.title = element_text(size = 24), | |
plot.subtitle = element_text(size = 18, color = "grey40"), | |
plot.caption = element_text(family = "Inconsolata", size = 16), | |
plot.margin = unit(rep(.5, 4), "cm") | |
) | |
ggsave( | |
p1, | |
filename = "covid19-peru-positivos-fallecidos-semanaepi.png", | |
height = 10, | |
width = 14 | |
) | |
p2 <- ggplot(comb) + | |
geom_point(aes(x = sunday_of_week, y = positivos_semana), color = "blue") + | |
geom_smooth(aes(x = sunday_of_week, y = positivos_semana), color = "blue", method = "gam") + | |
geom_point(aes(x = sunday_of_week, y = fallecidos_semana_scaled), color = "red") + | |
geom_smooth(aes(x = sunday_of_week, y = fallecidos_semana_scaled), color = "red", method = "gam") + | |
scale_y_continuous( | |
name = "Casos positivos", | |
labels = scales::comma, | |
sec.axis = sec_axis( | |
name = "Fallecidos", | |
trans = ~ . / factor, | |
labels = scales::comma | |
) | |
) + | |
scale_x_date( | |
name = "", | |
date_labels = "%b\n%Y", | |
date_breaks = "1 month" | |
) + | |
labs( | |
title = "COVID-19 (Perú): Casos positivos y fallecidos por semana epidemiológica", | |
subtitle = glue::glue("Fuente: Datos abiertos del MINSA, de {min_yw} a {max_yw}"), | |
caption = "Aproximación usando GAM [y ~ s(x, bs = 'cs')] - @jmcastagnetto, Jesus M. Castagnetto" | |
) + | |
theme_minimal(16) + | |
theme( | |
plot.background = element_rect(fill = "white"), | |
axis.title.y.left = element_text(color = "blue", size = 18, face = "bold"), | |
axis.text.y.left = element_text(color = "blue"), | |
axis.title.y.right = element_text(color = "red", size = 18, face = "bold"), | |
axis.text.y.right = element_text(color = "red"), | |
plot.title.position = "plot", | |
plot.title = element_text(size = 24), | |
plot.subtitle = element_text(size = 18, color = "grey40"), | |
plot.caption = element_text(family = "Inconsolata", size = 16), | |
plot.margin = unit(rep(.5, 4), "cm") | |
) | |
ggsave( | |
p2, | |
filename = "covid19-peru-positivos-fallecidos-semanaepi-gam.png", | |
height = 10, | |
width = 14 | |
) |
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Gráfico de líneas
Gráfico con aproximación usando GAM