02-data_acquisition.qmd

---
bibliography: references.bib
---
# Data Acquisition

## Import from lat / long file

The function `st_as_sf()` makes it possible to transform a `data.frame` container of geographic coordinates into an object `sf`. Here we use the `data.frame` `places2` created in the previous point.

```{r build_sf, eval = TRUE, echo = TRUE, nm = TRUE, fig.width=8, class.output="code-out", warning=FALSE, message=FALSE}
library(sf)
place_sf <- st_as_sf(read.csv("data_cambodia/adress.csv"), coords = c("long", "lat"), crs = 4326)
place_sf
```

To crate a `sf` POINT type object with only one pair of coordinate (WGS84, longitude=0.5, latitude = 45.5) :

```{r build_sf2, eval = TRUE, echo = TRUE, nm = TRUE, fig.width=8, class.output="code-out", warning=FALSE, message=FALSE}
library(sf)
test_point <- st_as_sf(data.frame(x = 0.5, y = 45.5), coords = c("x", "y"), crs = 4326)
test_point
```

We can display this object `sf` on an [OpenStreetMap](https://www.openstreetmap.org/) basesmap with the package maptiles `maptiles` [@maptiles].

```{r display_sf, eval = TRUE, echo = TRUE, nm = TRUE, out.width="788px", warning=FALSE, message=FALSE}
library(maptiles)
osm <- get_tiles(x = place_sf, zoom = 12)
plot_tiles(osm)
plot(st_geometry(place_sf), pch = 2, cex = 2, col = "red", add = TRUE)
```

## Online databases

## OpenStreetMap

::: {style="float: right"}
<img src="img/Openstreetmap_logo.svg" width="150px" padding="1em"/>
:::

[OpenStreetMap (OSM)](https://www.openstreetmap.org){target="_blank"} is a participatory mapping project that aim s to buil a free geographic database on a global scale. OpenStreetMap lets you view, edit and use geographic data around the world.

**Terms of use**

> OpenStreetMap is open data : you are free to use it for ant purpose as long as you credit OpenStreetMap and its contributers. If you modify or rely data in any way, you may distribute the result only under the same license. (...)

**Contributors**

> (...) Our contributors incloude enthusiastic mapmakers, GIS professional, engineers running OSM servers, humanitarians mapping disaster-stricken areas and many mmore.(...)

### Display and interactive map

The two main packages that allow to display as interactive map based on OSM are `leaflet` [@leaflet] and `mapview` [@mapview].

#### `leaflet`

<img src="img/logo_leaflet.png" align="right" width="200"/> `leaflet` uses the javascript library Leaflet [@JS-Leaflet] to create interactive maps.

```{r leaflet, eval=TRUE, cache = FALSE, class.output="code-out", warning=FALSE, message=FALSE}
library(sf)
library(leaflet)

district <- st_read("data_cambodia/cambodia.gpkg", layer = "district", quiet = TRUE)
hospital <- st_read("data_cambodia/cambodia.gpkg", layer = "hospital", quiet = TRUE)


banan <- district[district$ADM2_PCODE == "KH0201", ]     #Select one district (Banan district: KH0201)
health_banan <- hospital[hospital$DCODE == "201", ]      #Select Health centers in Banan

banan <- st_transform(banan, 4326)                       #Transform coordinate system to WGS84
health_banan <- st_transform(health_banan, 4326)

banan_map <- leaflet(banan) %>%                          #Create interactive map
  addTiles() %>%
  addPolygons() %>%
  addMarkers(data = health_banan)
banan_map
```

::: {.callout-note appearance="minimal" icon="false"}
Website of `leaflet`  
[Leaflet for R](https://rstudio.github.io/leaflet/)
:::

#### `mapview`

<img src="img/logo_mapview.gif" align="right" width="150"/> `mapview` relies on `leaflet` to create interactive maps, its use is easier and its documentation is a bit dense.

```{r mapview, cache=FALSE, class.output="code-out", warning=FALSE, message=FALSE}
library(mapview)
mapview(banan) + mapview(health_banan)
```

::: {.callout-note appearance="minimal" icon="false"}
Website of `mapview`  
[`mapview`](https://r-spatial.github.io/mapview/)
:::

### Import basemaps

The package `maptiles` [@maptiles] allows downlaoding and displaying raster basemaps.\
The function `get_tiles()` allow you to download OSM background maps and the function `plot_tiles()` allows to display them.\
Renders are better if the input data used the same coordinate system as the tiles ([EPSG:3857](https://github.com/riatelab/maptiles#projection)).

```{r display_point, fig.width=6, fig.height=6, eval=TRUE, class.output="code-out", warning=FALSE, message=FALSE}
library(sf)
library(maptiles)
district <- st_read("data_cambodia/cambodia.gpkg", layer = "district", quiet = TRUE)
district <- st_transform(district, 3857)
osm_tiles <- get_tiles(x = district, zoom = 10, crop = TRUE)
plot_tiles(osm_tiles)
plot(st_geometry(district), border = "grey20", lwd = .7, add = TRUE)
mtext(side = 1, line = -2, text = get_credit("OpenStreetMap"), col="tomato")
```