Projection of bubble/circle objects in maps - r

Question

I am attempting to do some basic concepts with mapping spatial data in R. I started with earthquakes to get some easy data to test with. I first downloaded an earthquake database from this link:
https://www.ngdc.noaa.gov/nndc/struts/results?type_0=Exact&query_0=$ID&t=101650&s=13&d=189&dfn=signif.txt
Then ran the following code to clean/organize this dataset:
library(dplyr)
library(tmap)
library(sf)
earthquake<-read.table("signif.txt",sep="\t",header=TRUE,fill=TRUE) %>% filter(!is.na(LATITUDE) & !is.na(LONGITUDE)) %>% st_as_sf(coords=c("LONGITUDE","LATITUDE"))
Then ran the following code to display a map of all magnitude 9 and greater earthquakes:
tmap_mode("view")
tm_shape(earthquake %>% filter(EQ_PRIMARY > 9))+tm_bubbles(size = "EQ_PRIMARY",col="red",popup.vars=c("EQ_PRIMARY"))
I get this error message since I never assigned a projection to the data: Currect projection of shape earthquake %>% filter(EQ_PRIMARY > 9) unknown. Long-lat (WGS84) is assumed. This is fine, and I get the attached picture:
The problem with this is that the magnitude of that earthquake in Alaska is actually 9.2 while the magnitude of the southern one in Chile is 9.5, yet the Alaska circle is visibly bigger! The bubble icons further from the equator are being projected and distorted under the Mercator projection.
So I try to change the projection of my data to LAEA:
st_crs(earthquake)<-"+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs "
But now when I run the same map as above, the circles are being displayed at a proper size but the basemap does not render since I guess tmap doesn't have a LAEA basemap? This is where I get lost.
As a sidenote this isn't a problem for plotting mode since I can obviously put my own layer underneath that shares the same projection and everything is dandy. My confusion comes in interacting with leaflet.
What's the solution here? I would like to use the nice Mercator map because it looks nice but I don't want things like symbols to be distorted by it. Do I need to define a new size column to counteract the Mercator distortion like earthquake %>% mutate(EQ_PRIMARY1 = EQ_PRIMARY / (abs(LATITUDE)+1)) but replaced with an actual researched function that would counteract the size effect? Is this a common issue in this area or is this something this package just doesn't do correctly?

Answer 1

I did find a bit of a work-around as I described by getting a scale factor for each point based on its latitude. Forgive me if this is a weird work-around but I'm a bit new to this. The basic procedure was:
Add two new geometries based on projection of the existing geometry - project one of them to EQC and one of them this same EQC projection but shifted upward 1 unit (I did this by setting false northing to 1 in the proj4). We basically want two geometries where one unit is one north of the other.
Transform these two geometries to the web mercator using st_transform.
Measure the y-distance between the resulting geometries. This is how much the Web Mercator scales 1 unit of distance at that particular latitude. It is very close to 1.000 for points close to the equator and nearly 2.5 near the poles.
Scale the size of the dots by the inverse square of the above factor.
Code looks like this:
earthquake$yeqc0<-earthquake %>% st_transform("+proj=eqc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=#null +wktext +no_defs") %>% st_geometry()
earthquake$yeqc1<-earthquake %>% st_transform("+proj=eqc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=1 +k=1.0 +units=m +nadgrids=#null +wktext +no_defs") %>% st_geometry()
Notice the subtle y_0=1 above.
st_crs(earthquake$yeqc1)<-st_crs(earthquake$yeqc0)
earthquake$ymerc<-st_distance(st_transform(earthquake$yeqc0,crs="+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=#null +wktext +no_defs"),st_transform(earthquake$yeqc1,crs="+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=#null +wktext +no_defs"),by_element=TRUE)
earthquake<-earthquake %>% mutate(EQ_PRIMARY1 = EQ_PRIMARY * (1 / ymerc)^2)
tm_shape(earthquake %>% filter(EQ_PRIMARY > 9))+tm_bubbles(size = "EQ_PRIMARY1",col="red",popup.vars=c("EQ_PRIMARY","EQ_PRIMARY1"))
This produces this map which has the dots as the proper size. The code is a little clunky but it could be worse I guess. Probably something that would merit a custom function if one doesn't exist.

Answer 2

First, you need to set the crs to the projection it is currently in, probably WGS84. Then use st_transform to change the coordinates. Here's the code, but it seems to be showing a similar result. Perhaps a different projection would work, or try changing the projection in the tm_shape function.
library(dplyr)
library(tmap)
library(sf)
earthquake<-read.table("https://www.ngdc.noaa.gov/nndc/struts/results?type_0=Exact&query_0=$ID&t=101650&s=13&d=189&dfn=signif.txt",
sep="\t",header=TRUE,fill=TRUE) %>%
filter(!is.na(LATITUDE) & !is.na(LONGITUDE)) %>%
st_as_sf(coords=c("LONGITUDE","LATITUDE"))
st_crs(earthquake) <- 4326
earthquake <- st_transform(earthquake, "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs ")
tmap_mode("view")
tm_shape(earthquake %>% filter(EQ_PRIMARY > 9))+
tm_bubbles(size = "EQ_PRIMARY",col="red",popup.vars=c("EQ_PRIMARY"))