all functions documented and can be built (with documentation) successfully in...

all functions documented and can be built (with documentation) successfully in Rstudio using -install and restart- and then devtools::document()

source/auto_crop.R

 #' auto_crop
 #'
-#' Measure the distance between foci on a synaptonemal complex
+#' crop an image around each viable cell candidate.
 #'
 #' @import EBImage
 #' @export
@@ -91,7 +91,7 @@ print("viable cells")
 
 #' get_blobs
 #'
-#' Measure the distance between foci on a synaptonemal complex
+#' Makes mask of all objects bright enough
 #'
 #' @import EBImage
 #' @export
@@ -132,7 +132,7 @@ get_blobs <- function(img_orig, crop_method = "regular"){
 
 #' keep_cells
 #'
-#' Measure the distance between foci on a synaptonemal complex
+#' Deletes objects in mask which are too small, large, oblong i.e. unlikely to be a cell
 #'
 #' @import EBImage
 #' @export
@@ -179,7 +179,7 @@ keep_cells <- function(candidate){
 
 #' crop_single_object
 #'
-#' Measure the distance between foci on a synaptonemal complex
+#' Creates mask for every individual cell candidate in mask
 #'
 #' @import EBImage
 #' @export

source/count_foci.R

 #' count_foci
 #'
-#' Measure the distance between foci on a synaptonemal complex
+#' Count coincident foci in cropped SC and foci channel per cell
 #'
 #' @import EBImage
 #' @export