diff --git a/r/dependencies.r b/r/dependencies.r
index 55eca24..97e1072 100644
--- a/r/dependencies.r
+++ b/r/dependencies.r
@@ -16,6 +16,7 @@ libs <- load_libs('dplyr',
                   'parallel',
                   'raster',
                   'rslurm',
+                  'R.utils',
                   lib.loc = lib.loc)
 
 # Load permute fortran dll for footprint matrix permutation
diff --git a/r/src/link_files.r b/r/src/link_files.r
index d728faf..61851ac 100644
--- a/r/src/link_files.r
+++ b/r/src/link_files.r
@@ -1,5 +1,5 @@
-#' link_files symlinks files in exe/* to the target path
-#' @author Ben Fasoli
+#' link_files symlinks files to the target path using relative paths
+#' @author Ben Fasoli & James Mineau
 #'
 #' @param from location of files
 #' @param to location to create links
@@ -7,6 +7,16 @@
 #' @export
 
 link_files <- function(from, to) {
-  files <- dir(from, full.names = T)
-  suppressWarnings(file.symlink(files, to))
+  require(R.utils)
+
+  # # Get all files in `from`
+  x <- lapply(from, list.files, full.names = T)
+  is_file <- sapply(x, function(x) length(x) == 0)
+  files <- c(from[is_file], unlist(x[!is_file]))
+
+  # Convert to paths relative to stilt_wd
+  relative_files <- R.utils::getRelativePath(files, to)
+
+  # Create the links
+  suppressWarnings(file.symlink(relative_files, to))
 }
diff --git a/r/src/simulation_step.r b/r/src/simulation_step.r
index e147ad8..425874a 100644
--- a/r/src/simulation_step.r
+++ b/r/src/simulation_step.r
@@ -330,9 +330,7 @@ simulation_step <- function(before_footprint = list(function() {output}),
       
       # Save output object to compressed rds file and symlink to out/particles
       saveRDS(output, output$file)
-      
-      link <- file.path(output_wd, 'particles', basename(output$file))
-      suppressWarnings(file.symlink(output$file, link))
+      link_files(output$file, file.path(output_wd, 'particles'))
       
     } else {
       # If user opted to recycle existing trajectory files, read in the recycled
@@ -381,8 +379,7 @@ simulation_step <- function(before_footprint = list(function() {output}),
     }
     
     # Symlink footprint to out/footprints
-    link <- file.path(output_wd, 'footprints', basename(foot_file))
-    suppressWarnings(file.symlink(foot_file, link))
+    link_files(foot_file, file.path(output_wd, 'footprints'))
 
     return(foot)
   })