---
title: "Get Semáforo Epidemiológico Data from Mexico COVID-19 Response"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Get Semáforo Epidemiológico Data from Mexico COVID-19 Response}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(semaforos)
```

```{r}
sl <- semaforos_get("long")
head(sl)
```


## Map of semaforos over time

```{r, dpi = 96, warning = FALSE, message = FALSE, out.width="30%"}
```{r, "maps-ggplot", dpi = 96, warning = FALSE, message = FALSE, out.width="30%"}
library(ggplot2)
library(sf)

mxstates <- readRDS(system.file("extdata", "sf_mx_estados.rds", package = "semaforos"))

df <- merge(mxstates, sl, by.x = "name", by.y = "estado", all = TRUE)
df$yearweek <- paste(df$year, df$week, sep = "-")

for (w in sort(unique(df$yearweek))) {
  print(
    ggplot(df[df$yearweek == w, ]) +
      geom_sf(aes(fill = color), size = 0.2) +
      coord_sf() +
      scale_fill_manual(values = c("verde" = "#02A247", "amarillo" = "#FFC60F", "naranja" = "#FF7000", "rojo" = "#FF0000"),
                        limits = c("verde", "amarillo", "naranja", "rojo")) +
      theme_minimal() +
      theme(title = element_text(color = "grey30"), legend.text = element_text(color = "grey30")) +
      labs(title = paste("Semáforos for week", w))
  )
}
```

## Duration of each semáforo

```{r}
library(dplyr)
library(ggplot2)

duration_sf <- sl %>%
  group_by(estado) %>%
  summarize(semaforo = rle(color)$values,
            duration = rle(color)$lengths)
head(duration_sf)

ggplot(duration_sf, aes(x = duration, fill = semaforo)) +
  geom_histogram() +
  scale_fill_manual(values = c("verde" = "#02A247", "amarillo" = "#FFC60F", "naranja" = "#FF7000", "rojo" = "#FF0000"),
                    limits = c("verde", "amarillo", "naranja", "rojo")) +
  labs(x = "duration (weeks)",
       title = "Distribution of the durations of semáforos in Mexico") +
  theme_minimal()

ggplot(duration_sf, aes(x = semaforo, y = duration, fill = semaforo, color = semaforo)) +
  geom_violin(alpha = 0.5) +
  geom_jitter() +
  scale_fill_manual(values = c("verde" = "#02A247", "amarillo" = "#FFC60F", "naranja" = "#FF7000", "rojo" = "#FF0000"),
                    limits = c("verde", "amarillo", "naranja", "rojo")) +
  scale_colour_manual(values = c("verde" = "#02A247", "amarillo" = "#FFC60F", "naranja" = "#FF7000", "rojo" = "#FF0000"),
                      limits = c("verde", "amarillo", "naranja", "rojo")) +
  labs(y = "duration (weeks)",
       title = "Duration of semáforos in Mexico depending on the colour") +
  theme_minimal()
```

## Time spent in each colour

```{r}
library(dplyr)
library(forcats)

sl %>%
  count(color, estado) %>%
  ggplot(aes(x = n, y = estado, fill = fct_relevel(color, "verde"))) +
    geom_histogram(stat = "identity") +
    scale_fill_manual(values = c("verde" = "#02A247", "amarillo" = "#FFC60F", "naranja" = "#FF7000", "rojo" = "#FF0000"),
                      limits = c("verde", "amarillo", "naranja", "rojo"),
                      name = "color") +
    theme_minimal() +
    labs(x = "total number of weeks on this colour")
```