Get phecode information

Either grabs a vector of descriptions for passed vector of phecodes, or vector of categories, or a dataframe with both.

get_phecode_info(codes, what = "description")

Arguments

codes	Vector of phecodes
what	What info should be returned. Options: 'description', 'category', 'all'.

Value

Vector of what is description or category, dataframe with phecode, description, and category if what = 'all'.

See also

get_phecode_info

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union

# Simulate some random data associated with phecodes
data_w_phecodes <- sample_n(phecode_descriptions, 100) %>%
  select(code = phecode) %>%
  mutate(random = rnorm(n()))

# Use function to add a column with description
data_w_phecodes %>%
  mutate(descrip = get_phecode_info(code, 'description'))
#> # A tibble: 100 x 3
#>    code   random descrip                                                        
#>    <chr>   <dbl> <chr>                                                          
#>  1 593.10  1.40  Gross hematuria                                                
#>  2 696.40 -0.679 Psoriasis                                                      
#>  3 292.40  0.738 Altered mental status                                          
#>  4 132.00 -0.861 Infestation (lice, mites)                                      
#>  5 300.90  0.421 Posttraumatic stress disorder                                  
#>  6 340.10  1.45  Migrain with aura                                              
#>  7 480.13  0.194 MRSA pneumonia                                                 
#>  8 931.00 -0.691 Contact dermatitis and other eczema due to plants [except food]
#>  9 600.00  1.34  Hyperplasia of prostate                                        
#> 10 225.00  2.74  Benign neoplasm of brain and other parts of nervous system     
#> # … with 90 more rows

# Use function to add column with category
data_w_phecodes %>%
  mutate(category = get_phecode_info(code, 'category'))
#> # A tibble: 100 x 3
#>    code   random category           
#>    <chr>   <dbl> <chr>              
#>  1 593.10  1.40  genitourinary      
#>  2 696.40 -0.679 dermatologic       
#>  3 292.40  0.738 mental disorders   
#>  4 132.00 -0.861 infectious diseases
#>  5 300.90  0.421 mental disorders   
#>  6 340.10  1.45  neurological       
#>  7 480.13  0.194 respiratory        
#>  8 931.00 -0.691 dermatologic       
#>  9 600.00  1.34  genitourinary      
#> 10 225.00  2.74  neoplasms          
#> # … with 90 more rows

# Use function to get dataframe of category and description that can be to join
# with data
bind_cols(
  data_w_phecodes,
  get_phecode_info(data_w_phecodes$code, 'all')
)
#> # A tibble: 100 x 5
#>    code   random phecode description                              category      
#>    <chr>   <dbl> <chr>   <chr>                                    <chr>         
#>  1 593.10  1.40  593.10  Gross hematuria                          genitourinary 
#>  2 696.40 -0.679 696.40  Psoriasis                                dermatologic  
#>  3 292.40  0.738 292.40  Altered mental status                    mental disord…
#>  4 132.00 -0.861 132.00  Infestation (lice, mites)                infectious di…
#>  5 300.90  0.421 300.90  Posttraumatic stress disorder            mental disord…
#>  6 340.10  1.45  340.10  Migrain with aura                        neurological  
#>  7 480.13  0.194 480.13  MRSA pneumonia                           respiratory   
#>  8 931.00 -0.691 931.00  Contact dermatitis and other eczema due… dermatologic  
#>  9 600.00  1.34  600.00  Hyperplasia of prostate                  genitourinary 
#> 10 225.00  2.74  225.00  Benign neoplasm of brain and other part… neoplasms     
#> # … with 90 more rows