Leaflet - europe spatial network plot and distanced island removal - r

Question

I probably have very complex question related to leaflet, I am trying to plot multile countries of Europe (data downloaded from GADM), and then create a network matrix for countries, however france contain island and for some reasons computation of weight matrix work, however when creating a dataframe of it, it cannon be created (when france is dropped data6 it works)
Is there a way how to delete that island from France data, or are there pager pages where can one get and easily plot countries like in my example?
also when france is dropped and map is created in leaflet there is a weird horizontal line, can it be somehow erased?
example down here (seem very long, but that is because of many country geodata)
library(leaflet)
library(ggplot2)
library(sf)
library(spdep)
library(leaflet.minicharts)
library(leafletCN)
# Regions of each country selected
URL <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_DEU_1_sp.rds"
data <- readRDS(url(URL))
URL2 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_CZE_1_sp.rds"
data2 <- readRDS(url(URL2))
URL3 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_POL_1_sp.rds"
data3 <- readRDS(url(URL3))
URL4 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_SVK_1_sp.rds"
data4 <- readRDS(url(URL4))
URL5 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_AUT_1_sp.rds"
data5 <- readRDS(url(URL5))
URL6 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_FRA_1_sp.rds"
data6 <- readRDS(url(URL6))
URL7 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_HUN_1_sp.rds"
data7 <- readRDS(url(URL7))
URL8 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_BEL_1_sp.rds"
data8 <- readRDS(url(URL8))
URL9 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_NLD_1_sp.rds"
data9 <- readRDS(url(URL9))
URL10 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_CHE_1_sp.rds"
data10 <- readRDS(url(URL10))
# Country borders of all countries
B_URL <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_DEU_0_sp.rds"
Bdata <- readRDS(url(B_URL))
B_URL2 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_CZE_0_sp.rds"
Bdata2 <- readRDS(url(B_URL2))
B_URL3 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_POL_0_sp.rds"
Bdata3 <- readRDS(url(B_URL3))
B_URL4 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_SVK_0_sp.rds"
Bdata4 <- readRDS(url(B_URL4))
B_URL5 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_AUT_0_sp.rds"
Bdata5 <- readRDS(url(B_URL5))
B_URL6 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_FRA_0_sp.rds"
Bdata6 <- readRDS(url(B_URL6))
B_URL7 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_HUN_0_sp.rds"
Bdata7 <- readRDS(url(B_URL7))
B_URL8 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_BEL_0_sp.rds"
Bdata8 <- readRDS(url(B_URL8))
B_URL9 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_NLD_0_sp.rds"
Bdata9 <- readRDS(url(B_URL9))
B_URL10 <- "https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_CHE_0_sp.rds"
Bdata10 <- readRDS(url(B_URL10))
# Trying to perform network base on QUEEN AND ROOK
A <- rbind(data, data2, data3, data4, data5,data6, data7, data8, data9, data10)
queen_data <- poly2nb(A, queen = F)
queen_data <- nb2listw(queen_data, style = "W", zero.policy = TRUE)
# Creating dataframe for plot purposes
data_df <- data.frame(coordinates(A))
colnames(data_df) <- c("long", "lat")
n = length(attributes(queen_data$neighbours)$region.id)
DA = data.frame(
from = rep(1:n,sapply(queen_data$neighbours,length)),
to = unlist(queen_data$neighbours),
weight = unlist(queen_data$weights)
)
DA = cbind(DA, data_df[DA$from,], data_df[DA$to,])
colnames(DA)[4:7] = c("long","lat","long_to","lat_to")
leaflet() %>% addProviderTiles("CartoDB.Positron") %>%
addPolygons(data=data, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data2, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data3, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data4, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data5, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data7, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data8, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data9, weight = 1, fill = F, color = "red") %>%
addPolygons(data=data10, weight = 1, fill = F, color = "red") %>%
addPolygons(data=Bdata, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata2, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata3, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata4, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata5, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata6, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata7, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata8, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata9, weight = 3, fill = F, color = "black") %>%
addPolygons(data=Bdata10, weight = 3, fill = F, color = "black") %>%
addCircles(lng = data_df$long, lat = data_df$lat, weight = 9) %>%
#addCircles(lng = data_df2$long, lat = data_df2$lat) %>%
addFlows(lng0 = DA$long, lat0 = DA$lat,lng1 = DA$long_to, lat1 = DA$lat_to,
dir = 0, maxThickness= 0.85)

Answer 1

I came up with mechanical solution where we would mechaniccaliy force data.frame to have same number of rows, however this approach is not good.
A <- rbind(data, data2, data3, data4, data5, data6, data7, data8, data9, data10)
queen_data <- poly2nb(A, queen = T)
queen_data <- nb2listw(queen_data, zero.policy = T)
plot(A)
plot(queen_data, coordinates(A), add = T, col = "red")
# Creating dataframe for plot purposes
data_df <- data.frame(coordinates(A))
colnames(data_df) <- c("long", "lat")
n = length(attributes(queen_data$neighbours)$region.id)
weights = unlist(queen_data$weights)
data_df[DA$from,] %>% dim()
da_to = data_df[DA$to,]
da_to[709, c(1, 2)] = NA
weight[709] = NA
DA = data.frame(
from = rep(1:n,sapply(queen_data$neighbours,length)),
to = unlist(queen_data$neighbours),
weight = weight
)
DA = cbind(DA, data_df[DA$from,], da_to)
colnames(DA)[4:7] = c("long","lat","long_to","lat_to")
final plot should look like plot(A) plot(queen_data, coordinates(A), add = T, col = "red") and when plotting this DA dataframe leaflet it is NOT the same and therefore not right.