如何使用 data.table 有效地计算一个数据集中的 GPS 点与另一数据集中的 GPS 点之间的距离

Question

I am facing a coding (optimization) problem in R. I have a long data set with GPS coordinates (lon, lat, timestamp) and for every row I need to check whether the location is near a bus stop. I have a .csv file with all the bus stops (in the Netherlands). The GPS coordinates file is millions of entries long, but could be split if necessary. The bus stop dataset is around 5500 entries long.
Using the code and tips given on, inter alia, these pages:

1) How to efficiently calculate distance between pair of coordinates using data.table :=

2) Using a simple for loop on spatial data

3) Calculate distance between two latitude-longitude points? (Haversine formula)

4) Fastest way to determine COUNTRY from millions of GPS coordinates [R]

I was able to construct a code that works, but is (too) slow. I was wondering if someone can help me with a faster data.table() implementation or can point out where the bottle neck in my code is? Is it the spDistsN1() function, or maybe the apply and melt() functions combination? I am most comfortable in R, but open to other software (as long as it is open source).

Due to privacy concerns I cannot upload the full dataset, but this is a (small) reproducible example that is not too different from how the real data looks.

# packages:
library(data.table)
library(tidyverse)
library(sp)


# create GPS data
number_of_GPS_coordinates <- 20000
set.seed(1)
gpsdata<-as.data.frame(cbind(id=1:number_of_GPS_coordinates, 
                             lat=runif(number_of_GPS_coordinates,50.5,53.5), 
                             lon=runif(number_of_GPS_coordinates,4,7)))

# create some busstop data. In this case only 2000 bus stops
set.seed(1)
number_of_bus_stops <- 2000
stop<-as.data.frame(gpsdata[sample(nrow(gpsdata), number_of_bus_stops), -1]) # of course do not keep id variable
stop$lat<-stop$lat+rnorm(number_of_bus_stops,0,.0005)
stop$lon<-stop$lon+rnorm(number_of_bus_stops,0,.0005)
busdata.data<-cbind(stop, name=replicate(number_of_bus_stops, paste(sample(LETTERS, 15, replace=TRUE), collapse="")))

names(busdata.data) <- c("latitude_bustops",  "longitude_bustops", "name")

Download the real bus stop data if you want, kind of hard to reproduce a random sample of this.

#temp <- tempfile()
#download.file("http://data.openov.nl/haltes/stops.csv.gz", temp) #1.7MB
#gzfile(temp, 'rt')
#busstopdata <- read.csv(temp, stringsAsFactors = FALSE)
#unlink(temp)
#bus_stops <- fread("bus_stops.csv")
#busdata.data <- busstopdata %>%
#  mutate(latitude_bustops = latitude)%>%
#  mutate(longitude_bustops = longitude)%>%
#  dplyr::select(name, latitude_bustops,  longitude_bustops)

Code I use now to calculate distances. It works but it is pretty slow

countDataPoints3 <- function(p) {
  distances <- spDistsN1(data.matrix(gpsdata[,c("lon","lat")]), 
                         p,
                         longlat=TRUE) # in km
  return(which(distances <= .2)) # distance is now set to 200 meters
}


# code to check per data point if a bus stop is near and save this per bus stop in a list entry
datapoints.by.bustation       <- apply(data.matrix(busdata.data[,c("longitude_bustops","latitude_bustops")]), 1, countDataPoints3)


# rename list entries
names(datapoints.by.bustation) <- busdata.data$name

# melt list into one big data.frame
long.data.frame.busstops       <- melt(datapoints.by.bustation)

# now switch to data.table grammar to speed up process
# set data.table
setDT(gpsdata)
gpsdata[, rowID := 1:nrow(gpsdata)]
setkey(gpsdata, key = "rowID")
setDT(long.data.frame.busstops)

# merge the data, and filter non-unique entries 
setkey(long.data.frame.busstops, key = "value")
GPS.joined        <- merge(x = gpsdata, y = long.data.frame.busstops, by.x= "rowID", by.y= "value", all.x=TRUE)
GPS.joined.unique <- unique(GPS.joined, by="id") # mak

# this last part of the code is needed to make sure that if there are more than 1 bus stop nearby it puts these bus stop in a list
# instead of adding row and making the final data.frame longer than the original one
GPS.joined.unique2 <- setDT(GPS.joined.unique)[order(id, L1), list(L1=list(L1)), by=id]
GPS.joined.unique2[, nearby := TRUE][is.na(L1), nearby := FALSE] # add a dummy to check if any bus stop is nearby.

# makes sense:
as.tibble(GPS.joined.unique2) %>%
  summarize(sum = sum(nearby)) 

Answer 1

Consider cutting using an slicing method: first cut by close latitudes and close longitudes. In this case 0.5 latitude and 0.5 longitude (which is still about a 60 km disc). We can use data.table 's superb support of rolling joins.

The following takes a few milliseconds for 20,000 entries and only a few seconds for 2M entries.

library(data.table)
library(hutils)
setDT(gpsdata)
setDT(busdata.data)

gps_orig <- copy(gpsdata)
busdata.orig <- copy(busdata.data)

setkey(gpsdata, lat)

# Just to take note of the originals
gpsdata[, gps_lat := lat + 0]
gpsdata[, gps_lon := lon + 0]

busdata.data[, lat := latitude_bustops + 0]
busdata.data[, lon := longitude_bustops + 0]


setkey(busdata.data, lat)

gpsID_by_lat <- 
  gpsdata[, .(id), keyby = "lat"]


By_latitude <- 
  busdata.data[gpsdata, 
               on = "lat",

               # within 0.5 degrees of latitude
               roll = 0.5, 
               # +/-
               rollends = c(TRUE, TRUE),

               # and remove those beyond 0.5 degrees
               nomatch=0L] %>%
  .[, .(id_lat = id,
        name_lat = name,
        bus_lat = latitude_bustops,
        bus_lon = longitude_bustops,
        gps_lat,
        gps_lon),
    keyby = .(lon = gps_lon)]

setkey(busdata.data, lon)

By_latlon <-
  busdata.data[By_latitude,
               on = c("name==name_lat", "lon"),

               # within 0.5 degrees of latitude
               roll = 0.5, 
               # +/-
               rollends = c(TRUE, TRUE),
               # and remove those beyond 0.5 degrees
               nomatch=0L]

By_latlon[, distance := haversine_distance(lat1 = gps_lat, 
                                           lon1 = gps_lon,
                                           lat2 = bus_lat,
                                           lon2 = bus_lon)]

By_latlon[distance < 0.2]

Answer 2

This is the function I came up with so far. @Dave2e, thanks. It is already an awful lot faster than what I had. There still is clearly room for a lot of improvement, but as it stands it is fast enough for my analysis now. I only slice by latitude and not longitude. The only reason for that is that it makes indexing and then looping over indices really easy, but more speed could be gained by also indexing by longitude. Also, in real GPS data there tend to be many duplicate values (same lon/lat, different time stamp), the code would also be more efficient if it would take this into account. Maybe I will work on that in the future.

# this app could be much faster if it would filter by duplicate GPS coordinates

check_if_close <- function(dataset1     = GPS.Utrecht.to.Gouda,       
                           dataset2     = bus_stops,     
                           n.splits     = 500,
                           desired.dist = .2){

# dataset1 needs at least the columns 
#  - "id", 
#  - "device_id"
#  - "latitude"
#  - "longitude"

# dataset2 needs at least the columns 
#  - "id", 
#  - "name"
#  - "latitude"
#  - "longitude"

# these are the average coordinates of the Netherlands. A change of ,.0017 in latitude leads to a change of 189 meters 
# spDistsN1(matrix(c(5.2913, 52.1326), ncol=2), matrix(c(5.2913, 52.1326+.0017), ncol=2), longlat=TRUE)*1000
# [1] 189.1604
# this means that the latitude slices we can cut (the subsection of) the Netherlands is have to be at least .0017 wide.
# if we look at the Netherlands a whole this would mean we can use max  (53.5-50.5)/.0017 = 1765 slices.
# if we look only at a small subsection (because we are only looking a a single trip for example we need much less slices.  

# 1) we only select the variables we need from dataset 1
  dataset1 <- setDT(dataset1)[,c("id", "device_id", "latitude", "longitude")]
  setnames(dataset1, old = c("id", "latitude", "longitude"), new = c("id_dataset1", "latitude_gps", "longitude_gps"))

# 2) we only select the variables we need from dataset 2
  dataset2 <- setDT(dataset2)[,c("id", "name", "latitude", "longitude")]
  setnames(dataset2, old = c("id", "latitude", "longitude"), new = c("id_dataset2", "latitude_feature", "longitude_feature"))

# 3) only keep subet of dataset2 that falls within dataset 1. 
#    There is no reason to check if features are close that already fall out of the GPS coordinates in the trip we want to check
#    We do add a 0.01 point margin around it to be on the save side. Maybe a feature falls just out the GPS coordinates, 
#    but is still near to a GPS point
  dataset2 <- dataset2[latitude_feature  %between%  (range(dataset1$latitude_gps) + c(-0.01, +0.01)) 
                       & longitude_feature %between% (range(dataset1$longitude_gps) + c(-0.01, +0.01)), ]

# 4) we cut the dataset2 into slices on the latitude dimension
#    some trial  and error is involved getting the right amount. if you add to many you get a large and redudant amount of empty values
#    if you add to few you get you need to check too many GPS to feauture distances per slice



dataset2[, range2 := as.numeric(Hmisc::cut2(dataset2$latitude_feature, g=n.splits))]

# 5) calculate the ranges of the slices we just created
ranges <- dataset2[,list(Min=min(latitude_feature), Max= max(latitude_feature)), by=range2][order(range2)]
setnames(ranges, old = c("range2", "Min", "Max"), new = c("latitude_range", "start", "end"))


# 6) now we assign too which slice every GPS coordinate in our dataset1 belongs
#    this is super fast when using data.table grammar
elements1 <- dataset1$latitude_gps
ranges <- setDT(ranges)[data.table(elements1), on = .(start <= elements1, end >=elements1)]
ranges[, rowID := seq_len(.N)]
dataset1[,rowID := seq_len(.N)]
setkey(dataset1, rowID)
setkey(ranges, rowID)
dataset1<-dataset1[ranges]

# 7) this is the actual function we use to check if a datapoint is nearby.
#    potentially there are faster function to do this??
checkdatapoint <- function(p, h, dist=desired.dist) {
  distances <- spDistsN1(data.matrix(filter(dataset1,latitude_range==h)[,c("longitude_gps","latitude_gps")]), 
                         p,
                         longlat=TRUE) # in km
  return(which(distances <= dist)) # distance is now set to 200 meters
}

# 8) we assign a ID to the dataset1 starting again at every slice.
#    we need this to later match the data again 
dataset1[, ID2 := sequence(.N), by = latitude_range]

# 9) here we loop over all the splits and for every point check if there is a feature nearby in the slice it falls in
#    to be on the save side we also check the slice left and right of it, just to make sure we do not miss features that
#    are nearby, but just fall in a different slice.
#         9a: create an empty list we fill with dataframes later 
TT<-vector("list", length=n.splits)
#         9b: loop over the number of slices using above defined function

for(i in 1:n.splits){
  datapoints.near.feature<-apply(data.matrix(dataset2[range2 %in% c(i-1,i, i+1), c("longitude_feature","latitude_feature")]), 1, checkdatapoint, h=i)
#         9c: if in that slice there was no match between a GPS coordinate and an nearby feature, we create an empty list input
    if(class(datapoints.near.feature)=="integer"|class(datapoints.near.feature)=="matrix"){
    TT[[i]] <-NULL
  } else {
#         9d: if there was a match we get a list of data point that are named
    names(datapoints.near.feature)    <- dataset2[range2 %in% c(i-1,i, i+1), name]
#         9e: then we 'melt' this list into  data.frame
    temp <- melt(datapoints.near.feature)
#         9f: then we transform it into a data.table and change the names
    setDT(temp)
    setnames(temp, old=c("value", "L1"), new= c("value", "feature_name"))
#         9h: then we only select the data point in dataset1 that fall in the current slice give them an 
#             ID and merge them with the file of nearby busstops
    gpsdata.f <- dataset1[latitude_range==i, ]
    gpsdata.f[, rowID2 := seq_len(.N)]
    setkey(gpsdata.f, key = "rowID2")
    setkey(temp, key = "value")
    GPS.joined.temp <- merge(x = gpsdata.f, y = temp, by.x= "rowID2", by.y= "value", all.x=TRUE)
#         9i: we only keep the unique entries and for every slice save them to the list
    GPS.joined.unique.temp <- unique(GPS.joined.temp, by=c("id_dataset1", "feature_name"))
    TT[[i]] <-  GPS.joined.unique.temp 
    cat(paste0(round(i/n.splits*100), '% completed'), " \r"); flush.console()


    #cat(i/n.splits*100, " \r"); flush.console()

  }

}

# 10) now we left join the original dataset and and the data point that are near a feature
finallist<- merge(x = dataset1, 
                  y = rbindlist(TT[vapply(TT, Negate(is.null), NA)]), 
                  by.x= "id_dataset1", 
                  by.y= "id_dataset1", 
                  all.x=TRUE)

# 11) we add a new logical variable to check if any bus stop is near
finallist[, nearby := TRUE][is.na(feature_name), nearby := FALSE] # add a dummy to check if any bus stop is nearby.

# 12) if a point is near multiple features at once these are listed in a vector,
#     instead of having duplicate rows with teh same id but different features
finallist <- unique(setDT(finallist)[order(id_dataset1, feature_name), list(feature_name=list(feature_name), id=id_dataset1, lat=latitude_gps.x, lon=longitude_gps.x, nearby=nearby), by=id_dataset1], by="id_dataset1")

return(finallist)
}