Replacing "rdgal" with a Data Frame in 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)