Rollup binary phecode pairs

Takes phecodes that have been coded without rollup - E.g. existance of code 008.10 does not imply the existance of 008.00 - and produces a rolledup version of the dataset. Works with plain patient-phecode pairs and also with patient-code-count triplets.

rollup_phecode_pairs(
  patient_code_counts,
  patient_col = patient,
  phecode_col = phecode
)

Arguments

patient_code_counts	Data containing patient ids, phecodes, and counts of those phecodes.
patient_col	Unquoted name of the column containing patient ids in passed patient_code_counts's dataframe.
phecode_col	Unquoted name of the column containing phecodes in passed dataframe.

Value

Dataframe in same format as passed patient_code_counts with code counts rolled up. This will most likely be longer than the original dataset because of the addition of potentially previously ommitted codes.

Examples

library(dplyr)

patient_data <- tribble(
  ~patient,    ~code,
         1, "250.23",
         1, "250.25",
         1, "696.42",
         1, "555.21",
         2, "401.22",
         2, "204.21",
         2, "735.22",
         2, "751.11",
)


# Also works with just binary occurance pairs
patient_data %>%
  rollup_phecode_pairs(patient_col = patient,
                  phecode_col = code)
#> # A tibble: 22 x 2
#>    patient code  
#>      <dbl> <chr> 
#>  1       1 250.23
#>  2       1 250.25
#>  3       1 696.42
#>  4       1 555.21
#>  5       2 401.22
#>  6       2 204.21
#>  7       2 735.22
#>  8       2 751.11
#>  9       1 250.20
#> 10       1 696.40
#> # … with 12 more rows