I have a dataset with animal records in different countries through a period of 13 years, the x y coordinates (in meters) and the year of the animal sighting. I want to know how to measure the distance in meters between the three closest neighbors from each point, but measuring this distance only within the points of the same year of survey. I want to find out which pairs of locations are closer than 1000m to each other and get a csv of these.
I am using package sf and I was able to estimate the distance between points but not sub-setting by year. I found that the package 'spatstat' could do this with 'nndist', however I found it complicated to set up the requested window and understanding the point pattern objects I need to work with. I am a newbie in R and it gets very complicated for me to be working with different type of objects and different packages, so I wonder if there is an easy way to do this in sf. I am open to suggestions on how to do this most efficiently though, if you suggest using another package or another way, please help me providing a code for transforming my data into the type of object needed for that package.
Thank you!
trial <-read.table(text =
"Country station_code lat_laea lon_laea year
Belize BF09-1 -2955950 1247610 2009
Belize BF09-10 -2953600 1248590 2009
Belize BF09-11 -2954620 1247900 2009
Belize BF11-13 -2958360 1244020 2011
Belize BF11-18 -2963740 1240290 2011
Belize BF11-19 -2963380 1242020 2011
Costa BraulioCarrilloNP-C16 -3640760 1821170 2011
Costa BraulioCarrilloNP-C17 -3640730 1823240 2011
Costa BraulioCarrilloNP-C18 -3642140 1817560 2011
Guatemala 40063 -3178260 1249780 2009
Guatemala 40596 -3183800 1246940 2009
Guatemala 43279 -3182640 1251560 2009",
header = TRUE)
trial.sp <- st_as_sf(trial, coords = c("lat_laea", "lon_laea"), crs = 3035)
plot(st_geometry(trial.sp))
test <- st_distance(trial.sp, trial.sp, by_element = FALSE, which = "Euclidean")
class(test)
test1 <- as.data.frame(test)
write_csv(test1, "test.csv")
What I would like is a csv file with all the pair of locations of the same year of study, which are closer than 1000m from each other.
The sf-package easily integrates into the dplyr-framework. This creates a circle with a radius of 1000 m around every point in trial.sp and joines it to the original dataset via the st_within-function.
trial.sp %>%
st_join(trial.sp %>% st_buffer(dist = 1000), join = st_within) %>%
filter(year.x == year.y)
This includes all stations that have no other station in 1000 m distance. They are just joined to itself. If you want to remove those you can do : filter(year.x == year.y & station_code.x != station_code.y)