Select a visit within a windowed chronogram

Usage

cg_select_visit(cg, visit_col = NULL, visit = c("earliest", "latest"))

Arguments

cg: a windowed chronogram
visit_col: a character vector to use to label the column with either dates of visits, or results. This is usually an experimental data column. Default is "NULL".
visit: either "earliest" or "latest"

Value

A subsetted chronogram

Examples

data(pitch_chronogram)

SevenDaysPrePostDose2 <- cg_window_by_metadata(
  pitch_chronogram, dose_2_date, 7, 7
)

SevenDaysPrePostDose2
#> # A tibble:     8,218 × 23
#> # A chronogram: try summary()
#>    calendar_date ID    Centre_code Previous_infection Vaccine_interval
#>  * <date>        <fct>       <int> <chr>              <chr>           
#>  1 2021-03-17    100             0 Y                  LONG            
#>  2 2021-03-18    100             0 Y                  LONG            
#>  3 2021-03-19    100             0 Y                  LONG            
#>  4 2021-03-20    100             0 Y                  LONG            
#>  5 2021-03-21    100             0 Y                  LONG            
#>  6 2021-03-22    100             0 Y                  LONG            
#>  7 2021-03-23    100             0 Y                  LONG            
#>  8 2021-03-24    100             0 Y                  LONG            
#>  9 2021-03-25    100             0 Y                  LONG            
#> 10 2021-03-26    100             0 Y                  LONG            
#> # ℹ 8,208 more rows
#> # ℹ 18 more variables: dose_1_date <date>, dose_2_date <date>, Victoria <int>,
#> #   Beta <int>, Gamma <int>, Delta <chr>, Cov2_RBD_MSD <dbl>,
#> #   Cov2_RBD_BAU <dbl>, Cov_2N_MSD <dbl>, Cov_2N_BAU <dbl>, Cov_2S_MSD <dbl>,
#> #   Cov_2S_BAU <dbl>, HKU1_S <dbl>, MERS_S <dbl>, NL63_S <dbl>, OC43_S <dbl>,
#> #   X229E_S <dbl>, Cov_1S <dbl>
#> # ★ Dates: calendar_date      ★ IDs: ID
#> # ★ metadata: Centre_code, Previous_infection, Vaccine_interval, dose_1_date, dose_2_date

## every visit has the assay `Cov_2S_MSD`
## therefore use this column to indicate a study visit 
SevenDaysPrePostDose2_visits <- cg_select_visit(
  SevenDaysPrePostDose2, Cov_2S_MSD, "earliest"
)

SevenDaysPrePostDose2_visits 
#> # A tibble:     22 × 23
#> # A chronogram: try summary()
#>    calendar_date ID    Centre_code Previous_infection Vaccine_interval
#>  * <date>        <fct>       <int> <chr>              <chr>           
#>  1 2021-04-10    1004            1 Y                  LONG            
#>  2 2021-02-12    1009            1 Y                  LONG            
#>  3 2021-03-30    1016            1 Y                  LONG            
#>  4 2021-02-05    1018            1 Y                  LONG            
#>  5 2021-03-15    1023            1 N                  LONG            
#>  6 2021-03-12    1027            1 N                  LONG            
#>  7 2021-03-28    1031            1 Y                  LONG            
#>  8 2021-03-22    1034            1 Y                  LONG            
#>  9 2021-03-10    1058            1 Y                  LONG            
#> 10 2021-02-10    1060            1 N                  SHORT           
#> # ℹ 12 more rows
#> # ℹ 18 more variables: dose_1_date <date>, dose_2_date <date>, Victoria <int>,
#> #   Beta <int>, Gamma <int>, Delta <chr>, Cov2_RBD_MSD <dbl>,
#> #   Cov2_RBD_BAU <dbl>, Cov_2N_MSD <dbl>, Cov_2N_BAU <dbl>, Cov_2S_MSD <dbl>,
#> #   Cov_2S_BAU <dbl>, HKU1_S <dbl>, MERS_S <dbl>, NL63_S <dbl>, OC43_S <dbl>,
#> #   X229E_S <dbl>, Cov_1S <dbl>
#> # ★ Dates: calendar_date      ★ IDs: ID
#> # ★ metadata: Centre_code, Previous_infection, Vaccine_interval, dose_1_date, dose_2_date

## all days without visits are now dropped. Compare:
nrow(SevenDaysPrePostDose2)
#> [1] 8218
nrow(SevenDaysPrePostDose2_visits)
#> [1] 22