index.qmd

---
title: "Geocoding of Diseases on the Iquitos - Nauta road, Loreto - Peru 📍🦟🛣️"
author: <i class="bi bi-people-fill"></i> Antony Barja & Bryan Fernandez, Innovalab - 2023 <img src='https://raw.githubusercontent.com/healthinnovation/innovar/master/man/figures/logo.png' width='40px'/>
mainfont: Roboto Slab
format: 
 html:
   toc: true
editor: visual
theme:
  light: flatly
  dark: darkly
---

## Requeriments

```{r}
#| echo: true
#| warning: false
#| message: false
library(tidyverse)
library(tidygeocoder)
library(sf)
library(leaflet)
library(cptcity)
```

## 1. Reading data processed

```{r}
#| warning: false
#| message: false
cases_reported <- read_csv('data/cases-report-geo-edited.csv')
```

```{r}
#| warning: false
#| message: false
cases_reported |> 
  DT::datatable(
    options = list(display = "compact", pageLength = 5, scrollX = TRUE)
  )
```

## 2. Geocoding with the MapBox API 
For use 100 000 request by month free.

Link: <https://www.mapbox.com/pricing/#search>

For to use MapBox API is necessary storage the personal TOKEN in the R environment. This step you can to do using the next code:

```
usethis::edit_r_environ()
MAPBOX_API_KEY="YourAPIKeyHere"

```

```{r}
#| warning: false
#| message: false
cases_reported |> 
    mutate(
     country = 'PERU',
     dep = 'LORETO',
     prov = 'MAYNAS',
     dist = 'SAN JUAN BAUTISTA',
     nogeo = sprintf(
       '%s,%s,%s,%s,%s,CENTRO POBLADO DE %s',
       country,
       dep,
       prov,
       dist,
       ccpp_name,
       str_to_upper(address)),
     geocode = geo(nogeo,method = "mapbox"),
     lat = geocode$lat,
     long = geocode$long
     ) |>
  select(-c(geocode)) -> geocode_cases_reported
```

```{r}
#| warning: false
#| message: false
geocode_cases_reported |> 
  DT::datatable(
    options = list(display = "compact", pageLength = 5, scrollX = TRUE)
  )
```

## 3. Analysis of geocoding data of diseases

```{r}
#| warning: false
#| message: false
stats <- geocode_cases_reported |>
  mutate(
    id_geocode = 
      case_when(
        is.na(lat) ~ 'No Geocoded',
        TRUE ~ 'Geocoded'
        )
    ) |> 
  group_by(id_geocode) |> 
  summarise(total = n()) |> 
  mutate(percentage = total*100/sum(total))
```

```{r}
#| warning: false
#| message: false
stats |> 
  ggplot(aes(x = id_geocode, y = percentage)) +
  geom_bar(stat = "identity", fill = '#086375',alpha = 0.5) + 
  geom_text(aes(label = round(percentage,2)),vjust= -0.5) + 
  theme_minimal()
```

## 4. No geocoding 

```{r}
#| warning: false
#| message: false
#| 
review_data <- geocode_cases_reported |> 
  filter(is.na(lat) | is.na(lat))
```

```{r}
#| warning: false
#| message: false
review_data |> 
  DT::datatable(
    options = list(display = "compact", pageLength = 5, scrollX = TRUE)
  )
```

## 5. Repair address 

- Replace "#"
- Remove "/AAHH LAS BRISAS2"
- Remove "N-"
- Replace "CA. " by CALLE
- Replace "AH " by ASENTAMIENTO HUMANO

```{r}
#| warning: false
#| message: false
review_data <- geocode_cases_reported |> 
  filter(is.na(lat) | is.na(lat)) |>
  mutate(
    address = gsub("#", "", address),
    address = gsub("/AAHH LAS BRISAS2", "", address),
    address = gsub("N-", "", address),
    address = gsub("CA. ", "CALLE ", address),
    address = gsub("AH", "ASENTAMIENTO HUMANO ", address),
    address = gsub("/AAHH", "ASENTAMIENTO HUMANO ", address),
    address = gsub("MZA.", "MZ ", address),
    address = gsub("AA. HH", "ASENTAMIENTO HUMANO ", address),
    address = gsub("/AASENTAMIENTO HUMANO H LAS BRISAS", " ASENTAMIENTO HUMANO LAS BRISAS", address)
  )
```

## 6. Geocoding with the MapBox API again

```{r}
#| warning: false
#| message: false
geocode_review_data <- review_data |> 
  mutate(
     country = 'PERU',
     dep = 'LORETO',
     prov = 'MAYNAS',
     dist = 'SAN JUAN BAUTISTA',
     nogeo = sprintf(
       '%s,%s,%s,%s,%s,CENTRO POBLADO DE %s',
       country,
       dep,
       prov,
       dist,
       ccpp_name,
       str_to_upper(address)),
     geocode = geo(nogeo,method = "mapbox"),
     lat = geocode$lat,
     long = geocode$long
     ) |>
  select(-c(geocode))
```

```{r}
#| warning: false
#| message: false
geocode_review_data |> 
  DT::datatable(
    options = list(display = "compact", pageLength = 5, scrollX = TRUE)
  )
```

## 7. Final dataset 

```{r}
#| warning: false
#| message: false
geocode_cases_reported_clean <- geocode_cases_reported |> 
  drop_na()

ddbb_geocoded <- bind_rows(
  geocode_cases_reported_clean,
  geocode_review_data)

ddbb_geocoded_sf <- ddbb_geocoded |>
  drop_na(lat,long) |> 
  st_as_sf(coords = c('lat','long'),crs = 4326)
```

## 8. Geovisualization

```{r}
#| warning: false
#| message: false
ddbb_geocoded |> 
  leaflet() |> 
  addTiles() |> 
  addMarkers()
```


## 9. Export final data 

```{r}
#| warning: false
#| message: false
write_csv(ddbb_geocoded,'output/cases_report_geocoded.csv')
write_sf(ddbb_geocoded_sf,'output/cases_report_geocoded.gpkg')
```