Create cohort from patient files
extract_cohort.RdCreate cohort from patient files
Arguments
- filepath
Path to directory containing .txt files.
- patids
Patids of patients to retain in the cohort. Character vector. Numeric values should not be used.
- select
Character vector of column names to select.
- set
If
TRUEwill create a variable calledsetwhich will contain the number that comes after the word 'set' in the file name.
Examples
## Extract cohort data
pat<-extract_cohort(filepath = system.file("aurum_data", package = "rcprd"))
pat
#> patid pracid usualgpstaffid gender yob mob emis_ddate regstartdate
#> 1 1 49 6 2 1984 NA 1976-11-21 1940-07-24
#> 2 2 79 11 1 1932 NA 1979-02-14 1929-02-23
#> 3 3 98 43 1 1930 NA 1972-06-01 1913-07-02
#> 4 4 53 72 2 1915 NA 1989-04-24 1969-07-11
#> 5 5 62 16 2 1916 NA 1951-09-23 1919-11-07
#> 6 6 54 11 1 1914 NA 1926-09-09 1970-08-28
#> 7 7 49 6 2 1984 NA 1976-11-21 1940-07-24
#> 8 8 79 11 1 1932 NA 1979-02-14 1929-02-23
#> 9 9 98 43 1 1930 NA 1972-06-01 1913-07-02
#> 10 10 53 72 2 1915 NA 1989-04-24 1969-07-11
#> 11 11 62 16 2 1916 NA 1951-09-23 1919-11-07
#> 12 12 54 11 1 1914 NA 1926-09-09 1970-08-28
#> patienttypeid regenddate acceptable cprd_ddate
#> 1 58 1996-08-25 1 1935-03-17
#> 2 21 1945-03-19 0 1932-02-05
#> 3 81 1997-04-24 1 1912-04-27
#> 4 10 1951-09-05 0 1921-02-13
#> 5 45 1998-11-25 0 1903-08-26
#> 6 85 1983-03-14 1 1963-08-27
#> 7 58 1996-08-25 1 1935-03-17
#> 8 21 1945-03-19 0 1932-02-05
#> 9 81 1997-04-24 1 1912-04-27
#> 10 10 1951-09-05 0 1921-02-13
#> 11 45 1998-11-25 0 1903-08-26
#> 12 85 1983-03-14 1 1963-08-27