Filter up to First PD (Progressive Disease) Date

Source: R/filter_pd.R

[Superseded] The filter_pd() function has been superseded in favor of filter_relative().

Filter a dataset to only include the source parameter records up to and including the first PD (progressive disease). These records are passed to downstream derivations regarding responses such as BOR (best overall response).

filter_pd(
  dataset,
  filter,
  source_pd,
  source_datasets,
  subject_keys = get_admiral_option("subject_keys")
)

Arguments

dataset

Input dataset

The variables ADT and those specified by subject_keys are expected.

filter

Filter condition for restricting the input dataset

source_pd

A admiral::date_source() object providing the date of first PD

For each subject the first date (date field) in the provided dataset (dataset_name field) restricted by filter field is considered as first PD date.

source_datasets

A named list of data sets is expected.

The name must match the name provided by the dataset_name field of the admiral::date_source() object specified for source_pd.

subject_keys

Variables to uniquely identify a subject

A list of symbols created using exprs() is expected.

Value

A subset of the input dataset

Details

  1. The input dataset (dataset) is restricted by filter.

  2. For each subject the first PD date is derived as the first date (source_pd$date) in the source pd dataset (source_datasets[[source_pd$dataset_name]]) restricted by source_pd$filter.

  3. The restricted input dataset is restricted to records up to first PD date. Records matching first PD date are included. For subject without any first PD date, all records are included.

Author

Teckla Akinyi, Stefan Bundfuss

Examples


library(dplyr)
library(lubridate)
library(admiral)
library(admiralonco)

# Filter OVR records up to first PD, first PD date provided in separate BDS dataset (adevent)
adrs <- tibble::tribble(
  ~STUDYID,       ~USUBJID,      ~PARAMCD, ~AVALC, ~ADT,         ~ANL01FL,
  "CDISCPILOT01", "01-701-1015", "OVR",    "CR",   "2016-01-25", "Y",
  "CDISCPILOT01", "01-701-1015", "OVR",    "SD",   "2016-02-22", NA_character_,
  "CDISCPILOT01", "01-701-1015", "OVR",    "PD",   "2016-02-22", "Y",
  "CDISCPILOT01", "01-701-1015", "BOR",    "CR",   "2016-01-25", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "SD",   "2015-12-07", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "PD",   "2016-04-25", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "PD",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1034", "BOR",    "SD",   "2015-12-07", "Y",
  "CDISCPILOT01", "01-701-1035", "OVR",    "SD",   "2016-04-25", "Y",
  "CDISCPILOT01", "01-701-1035", "OVR",    "PR",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1035", "BOR",    "PR",   "2016-06-25", "Y"
) %>% mutate(
  ADT = as_date(ADT)
)

adevent <- tibble::tribble(
  ~STUDYID,       ~USUBJID,      ~PARAMCD, ~AVALC, ~ADT,
  "CDISCPILOT01", "01-701-1015", "PD",     "Y",    "2016-02-22",
  "CDISCPILOT01", "01-701-1034", "PD",     "Y",    "2016-04-25"
) %>% mutate(
  ADT = as_date(ADT)
)

pd <- date_source(
  dataset_name = "adevent",
  date = ADT,
  filter = PARAMCD == "PD"
)

filter_pd(
  dataset = adrs,
  filter = PARAMCD == "OVR" & ANL01FL == "Y",
  source_pd = pd,
  source_datasets = list(adevent = adevent)
)
#> # A tibble: 6 × 6
#>   STUDYID      USUBJID     PARAMCD AVALC ADT        ANL01FL
#>   <chr>        <chr>       <chr>   <chr> <date>     <chr>  
#> 1 CDISCPILOT01 01-701-1015 OVR     CR    2016-01-25 Y      
#> 2 CDISCPILOT01 01-701-1015 OVR     PD    2016-02-22 Y      
#> 3 CDISCPILOT01 01-701-1034 OVR     SD    2015-12-07 Y      
#> 4 CDISCPILOT01 01-701-1034 OVR     PD    2016-04-25 Y      
#> 5 CDISCPILOT01 01-701-1035 OVR     SD    2016-04-25 Y      
#> 6 CDISCPILOT01 01-701-1035 OVR     PR    2016-06-25 Y      

# Filter OVR records up to first PD, first PD date provided in ADSL dataset
adsl <- tibble::tribble(
  ~STUDYID,       ~USUBJID,      ~PDDT,
  "CDISCPILOT01", "01-701-1015", "2016-02-22",
  "CDISCPILOT01", "01-701-1034", "2016-04-25",
  "CDISCPILOT01", "01-701-1035", ""
) %>% mutate(
  PDDT = as_date(PDDT)
)

pd <- date_source(
  dataset_name = "adsl",
  date = PDDT
)

filter_pd(
  dataset = adrs,
  filter = PARAMCD == "OVR" & ANL01FL == "Y",
  source_pd = pd,
  source_datasets = list(adsl = adsl)
)
#> # A tibble: 6 × 6
#>   STUDYID      USUBJID     PARAMCD AVALC ADT        ANL01FL
#>   <chr>        <chr>       <chr>   <chr> <date>     <chr>  
#> 1 CDISCPILOT01 01-701-1015 OVR     CR    2016-01-25 Y      
#> 2 CDISCPILOT01 01-701-1015 OVR     PD    2016-02-22 Y      
#> 3 CDISCPILOT01 01-701-1034 OVR     SD    2015-12-07 Y      
#> 4 CDISCPILOT01 01-701-1034 OVR     PD    2016-04-25 Y      
#> 5 CDISCPILOT01 01-701-1035 OVR     SD    2016-04-25 Y      
#> 6 CDISCPILOT01 01-701-1035 OVR     PR    2016-06-25 Y      

# Filter OVR records up to first PD, first PD date provided in input dataset (PD parameter)
adrs <- tibble::tribble(
  ~STUDYID,       ~USUBJID,      ~PARAMCD, ~AVALC, ~ADT,         ~ANL01FL,
  "CDISCPILOT01", "01-701-1015", "OVR",    "CR",   "2016-01-25", "Y",
  "CDISCPILOT01", "01-701-1015", "OVR",    "SD",   "2016-02-22", NA_character_,
  "CDISCPILOT01", "01-701-1015", "OVR",    "PD",   "2016-02-22", "Y",
  "CDISCPILOT01", "01-701-1015", "BOR",    "CR",   "2016-01-25", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "SD",   "2015-12-07", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "PD",   "2016-04-25", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "PD",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1034", "BOR",    "SD",   "2015-12-07", "Y",
  "CDISCPILOT01", "01-701-1035", "OVR",    "SD",   "2016-04-25", "Y",
  "CDISCPILOT01", "01-701-1035", "OVR",    "PR",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1035", "BOR",    "PR",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1015", "PD",     "Y",    "2016-02-22", "Y",
  "CDISCPILOT01", "01-701-1034", "PD",     "Y",    "2016-04-25", "Y"
) %>% mutate(
  ADT = as_date(ADT)
)

pd <- date_source(
  dataset_name = "adrs",
  date = ADT,
  filter = PARAMCD == "PD"
)

filter_pd(
  dataset = adrs,
  filter = PARAMCD == "OVR" & ANL01FL == "Y",
  source_pd = pd,
  source_datasets = list(adrs = adrs)
)
#> # A tibble: 6 × 6
#>   STUDYID      USUBJID     PARAMCD AVALC ADT        ANL01FL
#>   <chr>        <chr>       <chr>   <chr> <date>     <chr>  
#> 1 CDISCPILOT01 01-701-1015 OVR     CR    2016-01-25 Y      
#> 2 CDISCPILOT01 01-701-1015 OVR     PD    2016-02-22 Y      
#> 3 CDISCPILOT01 01-701-1034 OVR     SD    2015-12-07 Y      
#> 4 CDISCPILOT01 01-701-1034 OVR     PD    2016-04-25 Y      
#> 5 CDISCPILOT01 01-701-1035 OVR     SD    2016-04-25 Y      
#> 6 CDISCPILOT01 01-701-1035 OVR     PR    2016-06-25 Y      

# Filter OVR records up to first PD, first PD date derived from OVR records
adrs <- tibble::tribble(
  ~STUDYID,       ~USUBJID,      ~PARAMCD, ~AVALC, ~ADT,         ~ANL01FL,
  "CDISCPILOT01", "01-701-1015", "OVR",    "CR",   "2016-01-25", "Y",
  "CDISCPILOT01", "01-701-1015", "OVR",    "SD",   "2016-02-22", NA_character_,
  "CDISCPILOT01", "01-701-1015", "OVR",    "PD",   "2016-02-22", "Y",
  "CDISCPILOT01", "01-701-1015", "BOR",    "CR",   "2016-01-25", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "SD",   "2015-12-07", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "PD",   "2016-04-25", "Y",
  "CDISCPILOT01", "01-701-1034", "OVR",    "PD",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1034", "BOR",    "SD",   "2015-12-07", "Y",
  "CDISCPILOT01", "01-701-1035", "OVR",    "SD",   "2016-04-25", "Y",
  "CDISCPILOT01", "01-701-1035", "OVR",    "PR",   "2016-06-25", "Y",
  "CDISCPILOT01", "01-701-1035", "BOR",    "PR",   "2016-06-25", "Y"
) %>% mutate(
  ADT = as_date(ADT)
)

pd <- date_source(
  dataset_name = "adrs",
  date = ADT,
  filter = PARAMCD == "OVR" & ANL01FL == "Y" & AVALC == "PD"
)

filter_pd(
  dataset = adrs,
  filter = PARAMCD == "OVR" & ANL01FL == "Y",
  source_pd = pd,
  source_datasets = list(adrs = adrs)
)
#> # A tibble: 6 × 6
#>   STUDYID      USUBJID     PARAMCD AVALC ADT        ANL01FL
#>   <chr>        <chr>       <chr>   <chr> <date>     <chr>  
#> 1 CDISCPILOT01 01-701-1015 OVR     CR    2016-01-25 Y      
#> 2 CDISCPILOT01 01-701-1015 OVR     PD    2016-02-22 Y      
#> 3 CDISCPILOT01 01-701-1034 OVR     SD    2015-12-07 Y      
#> 4 CDISCPILOT01 01-701-1034 OVR     PD    2016-04-25 Y      
#> 5 CDISCPILOT01 01-701-1035 OVR     SD    2016-04-25 Y      
#> 6 CDISCPILOT01 01-701-1035 OVR     PR    2016-06-25 Y