Derive Affected Eye

Derive Affected Eye (AFEYE) in occurrence datasets

Usage

derive_var_afeye(
  dataset,
  dataset_occ,
  loc_var,
  lat_var,
  lat_vals,
  loc_vals = "EYE"
)

Arguments

dataset

Input dataset

dataset_occ

Input dataset

Please use dataset instead.

loc_var

Location variable

lat_var

Laterality variable

lat_vals

xxLATvalues for which AFEYE is derived

Please simply ensure xxLAT values are contained in c("LEFT", "RIGHT", "BILATERAL").

loc_vals

xxLOC values for which AFEYE is derived

Value

The input occurrence dataset with Affected Eye (AFEYE) added.

Details

Affected Eye is derived in the occurrence dataset using laterality and Study Eye. This assumes Study Eye has already been added from ADSL.

Author

Lucy Palmen

Examples

library(tibble)
library(admiral)

adae1 <- tribble(
  ~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT,
  "XXX001", "P01", "RIGHT", "EYE", "RIGHT",
  "XXX001", "P01", "RIGHT", "EYE", "LEFT",
  "XXX001", "P01", "RIGHT", "EYE", "",
  "XXX001", "P01", "RIGHT", "", "RIGHT",
  "XXX001", "P02", "LEFT", "", "",
  "XXX001", "P02", "LEFT", "EYE", "LEFT",
  "XXX001", "P04", "BILATERAL", "EYE", "RIGHT",
  "XXX001", "P05", "RIGHT", "EYE", "RIGHT",
  "XXX001", "P05", "RIGHT", "EYE", "BILATERAL",
  "XXX001", "P06", "BILATERAL", "", "",
  "XXX001", "P06", "BILATERAL", "", "RIGHT",
  "XXX001", "P07", "BILATERAL", "EYE", "BILATERAL",
  "XXX001", "P08", "", "EYE", "BILATERAL",
  "XXX001", "P09", "NONSENSE", "EYE", "BILATERAL",
  "XXX001", "P09", "BILATERAL", "EYE", "NONSENSE",
  "XXX001", "P09", "BILATERAL", "NONSENSE", "BILATERAL",
  "XXX001", "P10", "RIGHT", "EYE", "BOTH"
)

derive_var_afeye(adae1, loc_var = AELOC, lat_var = AELAT)
#> # A tibble: 17 × 6
#>    STUDYID USUBJID STUDYEYE    AELOC      AELAT       AFEYE     
#>    <chr>   <chr>   <chr>       <chr>      <chr>       <chr>     
#>  1 XXX001  P01     "RIGHT"     "EYE"      "RIGHT"     Study Eye 
#>  2 XXX001  P01     "RIGHT"     "EYE"      "LEFT"      Fellow Eye
#>  3 XXX001  P01     "RIGHT"     "EYE"      ""          NA        
#>  4 XXX001  P01     "RIGHT"     ""         "RIGHT"     NA        
#>  5 XXX001  P02     "LEFT"      ""         ""          NA        
#>  6 XXX001  P02     "LEFT"      "EYE"      "LEFT"      Study Eye 
#>  7 XXX001  P04     "BILATERAL" "EYE"      "RIGHT"     Study Eye 
#>  8 XXX001  P05     "RIGHT"     "EYE"      "RIGHT"     Study Eye 
#>  9 XXX001  P05     "RIGHT"     "EYE"      "BILATERAL" Both Eyes 
#> 10 XXX001  P06     "BILATERAL" ""         ""          NA        
#> 11 XXX001  P06     "BILATERAL" ""         "RIGHT"     NA        
#> 12 XXX001  P07     "BILATERAL" "EYE"      "BILATERAL" Both Eyes 
#> 13 XXX001  P08     ""          "EYE"      "BILATERAL" NA        
#> 14 XXX001  P09     "NONSENSE"  "EYE"      "BILATERAL" NA        
#> 15 XXX001  P09     "BILATERAL" "EYE"      "NONSENSE"  NA        
#> 16 XXX001  P09     "BILATERAL" "NONSENSE" "BILATERAL" NA        
#> 17 XXX001  P10     "RIGHT"     "EYE"      "BOTH"      NA        

adae2 <- tribble(
  ~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT,
  "XXX001", "P01", "RIGHT", "EYES", "RIGHT",
  "XXX001", "P02", "RIGHT", "RETINA", "LEFT",
  "XXX001", "P03", "LEFT", "", ""
)

derive_var_afeye(adae2, loc_var = AELOC, lat_var = AELAT, loc_vals = c("EYES", "RETINA"))
#> # A tibble: 3 × 6
#>   STUDYID USUBJID STUDYEYE AELOC    AELAT   AFEYE     
#>   <chr>   <chr>   <chr>    <chr>    <chr>   <chr>     
#> 1 XXX001  P01     RIGHT    "EYES"   "RIGHT" Study Eye 
#> 2 XXX001  P02     RIGHT    "RETINA" "LEFT"  Fellow Eye
#> 3 XXX001  P03     LEFT     ""       ""      NA