How to find the nearest distance between two diffe

I am trying to find the nearest distance of locations in dataset 1 to dataset 2. Both data sets are different sizes. Ive looked into using the Haversine function but I'm unsure what I need to do after.

Since you have not provided a sample of your data, I am going to use the oregon.tract data set from the UScensus2000tract library as a reproducible example.

Here is a solution based on fast data.table that I get from this other answer here.

# load libraries
  library(data.table)
  library(geosphere)
  library(UScensus2000tract)
  library(rgeos)

Now let's create a new data.table with all possible pair combinations of origins (census centroids) and destinations (facilities)

# get all combinations of origin and destination pairs
# Note that I'm considering here that the distance from A -> B is equal 
from B -> A.
  odmatrix <- CJ(Datatwo$Code_A , Dataone$Code_B)
  names(odmatrix) <- c('Code_A', 'Code_B') # update names of columns

# add coordinates of Datatwo centroids (origin)
  odmatrix[Datatwo, c('lat_orig', 'long_orig') := list(i.Latitude, 
i.Longitude), on= "Code_A" ]

# add coordinates of facilities (destination)
  odmatrix[Dataone, c('lat_dest', 'long_dest') := list(i.Latitude,  
i.Longitude), on= "Code_B" ]


Now you just need to:

# calculate distances
  odmatrix[ , dist := distHaversine(matrix(c(long_orig, lat_orig), ncol 
= 2), 
                                    matrix(c(long_dest, lat_dest), ncol  
= 2))]

# and get the nearest destinations for each origin
  odmatrix[, .(  Code_B = Code_B[which.min(dist)],
                    dist = min(dist)), 
                                    by = Code_A]

### Prepare data for this reproducible example
# load data
  data("oregon.tract")

# get centroids as a data.frame
  centroids <- as.data.frame(gCentroid(oregon.tract,byid=TRUE))

# Convert row names into first column
  setDT(centroids, keep.rownames = TRUE)[]

# get two data.frames equivalent to your census and facility data 
frames
  Datatwo<- copy(centroids)
  Dataone <- copy(centroids)

  names(Datatwo) <- c('Code_A', 'Longitude', 'Latitude')
  names(Dataone) <- c('Code_B', 'Longitude', 'Latitude')