Replacing "rdgal" with a Data Frame in R? - r

Question

I found this R code (Search button for Leaflet R map?) and was able to make a interactive map in R:
library(inlmisc)
city <- rgdal::readOGR(system.file("extdata/city.geojson",
package = "inlmisc")[1])
opt <- leaflet::markerClusterOptions(showCoverageOnHover = FALSE)
map <- CreateWebMap("Topo")
map <- leaflet::addMarkers(map, label = ~name, popup = ~name,
clusterOptions = opt,
clusterId = "cluster",
group = "marker", data = city)
map <- AddHomeButton(map)
map <- AddClusterButton(map, clusterId = "cluster")
map <- AddSearchButton(map, group = "marker", zoom = 15,
textPlaceholder = "Search city names...")
map
I was curious and wanted to see the format and entries of the "city" file. I was expecting this file to be a "tabular" file (i.e. containing rows and columns, like a data frame), but when I opened the file, it did not appear in this format at all - this file is apparently a "SpatialPointsDataFrame":
> head(city)
class : SpatialPointsDataFrame
features : 6
extent : -123.09, -73.8, 31.58, 44.62 (xmin, xmax, ymin, ymax)
crs : +proj=longlat +datum=WGS84 +no_defs
variables : 2
names : name, capital
min values : Abilene TX, 0
max values : Albany OR, 2
I then found this post here (How to convert a spatial dataframe back to normal dataframe?) and saw that you can convert a SpatialPointsDataFrame into a regular data frame like this:
DF <- as.data.frame(city)
> head(DF)
name capital coords.x1 coords.x2
1 Abilene TX 0 -99.74 32.45
2 Akron OH 0 -81.52 41.08
3 Alameda CA 0 -122.26 37.77
4 Albany GA 0 -84.18 31.58
5 Albany NY 2 -73.80 42.67
6 Albany OR 0 -123.09 44.62
But is there a way to convert a regular data frame into a "SpatialDataFrame"? I tried the following code and then tried to plot the results:
#https://stackoverflow.com/questions/29736577/how-to-convert-data-frame-to-spatial-coordinates
library(sf)
city <- st_as_sf(x = DF,
coords = c("coords.x1", "coords.x2"),
crs = "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")
map <- CreateWebMap("Topo")
map <- leaflet::addMarkers(map, label = ~name, popup = ~name,
clusterOptions = opt,
clusterId = "cluster",
group = "marker", data = city)
map <- AddHomeButton(map)
map <- AddClusterButton(map, clusterId = "cluster")
map <- AddSearchButton(map, group = "marker", zoom = 15,
textPlaceholder = "Search city names...")
map
The code ran, but I get this warning message:
Warning message:
sf layer has inconsistent datum (+proj=longlat +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +no_defs).
Need '+proj=longlat +datum=WGS84
Am I doing this correctly?
Thank you!

Answer 1

Leaflet uses a slightly different format of crs than sf with st_as_sf, which you can read more about on GitHub. You have a few options, where first we could use a shortened crs, like here:
library(sf)
city <- st_as_sf(x = DF,
coords = c("coords.x1", "coords.x2"),
crs = "+proj=longlat +datum=WGS84 +no_defs")
Or you can use sp::CRS along with your crs definition, so that it is properly read by leaflet:
city <- st_as_sf(x = DF,
coords = c("coords.x1", "coords.x2"),
crs = sp::CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"))
Or another option would be to use the SRID 4326 as the crs (which will set the Geodetic CRS):
city <- st_as_sf(x = DF,
coords = c("coords.x1", "coords.x2"),
crs = 4326)
map <- CreateWebMap("Topo")
map <- leaflet::addMarkers(map, label = ~name, popup = ~name,
clusterOptions = opt,
clusterId = "cluster",
group = "marker", data = city)
map <- AddHomeButton(map)
map <- AddClusterButton(map, clusterId = "cluster")
map <- AddSearchButton(map, group = "marker", zoom = 15,
textPlaceholder = "Search city names...")
map
You will notice that in the answer you are using that they are using mapview, which does work with the format that you give (i.e., crs = "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"). So, it would work with your code, but it won't be in the leaflet style:
city <- st_as_sf(x = DF,
coords = c("coords.x1", "coords.x2"),
crs = "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")
mapview::mapview(city)