Mapping Bus Routes with Leaflet in R - r

Question

I recently found this shape file of NYC bus routes shape file of NYC bus routes (zip file) that I am interested in plotting with the leaflet package in R.
When I attempt to do so, some routes do not show up on the map. I can tell they're missing because I overlay the bus stop data and some do not line up with the routes.
When I read in the shape file, I notice that the spatial lines data frame that is created has nested lists, which I think leaflet is not mapping.
What do I need to do so that leaflet reads coordinates of these missing routes? Below is the code I used to produce the map with missing routes:
bus <- readOGR(dsn = path.expand("bus_route_shapefile"), layer = "bus_route_shapefile")
bus.pj <- spTransform(bus, CRS("+proj=longlat +datum=WGS84"))
bus.st <- readOGR(dsn = path.expand("bus_stop_shapefile"), layer = "bus_stop_shapefile")
bus.st.pj <- spTransform(bus.st, CRS("+proj=longlat +datum=WGS84"))
bus_map <- leaflet() %>%
setView(lng = -73.932667, lat = 40.717266, zoom = 11) %>%
addPolylines(data = bus.pj, color = "black", opacity = 1) %>%
addCircles(data=bus.st.pj#data,~stop_lon, ~stop_lat, color = "red") %>%
addTiles()
bus_map

Answer 1

It would be easier to help you if you provided not only bus_routes but also bus_stop (zip file). You can solve it by converting bus.pj into new SpatialLinesxxx obj where each class Lines has only one class Line. SLDF below code makes doesn't have bus.pj#data$trip_heads because of unknown.
library(dplyr); library(sp); library(leaflet)
## resolve bus.pj#lines into list(Line.objs) (Don't worry about warnings)
Line_list <- lapply(bus.pj#lines, getLinesLinesSlot) %>% unlist()
## If you want just Lines infromation, finish with this line.
SL <- sapply(1:length(Line_list), function(x) Lines(Line_list[[x]], ID = x)) %>%
SpatialLines()
## make new ids (originalID_nth)
ori_id <- getSLLinesIDSlots(bus.pj) # get original ids
LinLS <- sapply(bus.pj#lines, function(x) length(x#Lines)) # how many Line.obj does each Lines.obj has
new_id <- sapply(1:length(LinLS), function(x) paste0(x, "_", seq.int(LinLS[[x]]))) %>%
unlist()
## make a new data.frame (only route_id)
df <- data.frame(route_id = rep(bus.pj#data$route_id, times = LinLS))
rownames(df) <- new_id
## integrate Line.objs, ids and a data.frame into SpatialLinesDataFrame.obj
SLDF <- mapply(function(x, y) Lines(x, ID = y), x = Line_list, y = new_id) %>%
SpatialLines() %>% SpatialLinesDataFrame(data = df)
leaflet() %>%
setView(lng = -73.932667, lat = 40.717266, zoom = 11) %>%
addPolylines(data = SLDF, color = "black", opacity = 1, weight = 1) %>%
addCircles(data=bus.st.pj#data,~stop_lon, ~stop_lat, color = "red", weight = 0.3)